Compositions and methods for improving sample identification in indexed nucleic acid libraries

ABSTRACT

The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by modifying or blocking 5′ and 3′ ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.

RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No.62/488,833, filed on Apr. 23, 2017, which application is herebyincorporated herein by reference.

FIELD

The present disclosure relates to, among other things, sequencing ofpolynucleotides from multiple libraries; and more particularly toincreasing the likelihood that sequencing properly identifies thelibrary from which the polynucleotides originated.

BACKGROUND

Improvements in sequencing methodologies have allowed for sequencing ofpooled or multiplexed polynucleic acids from different libraries in asingle sequencing protocol. A library-specific sequence (an “index tag”)may be added to polynucleic acids of each library so that the origin ofeach sequenced polynucleic acid may be properly identified. The indextag sequence may be added to polynucleic acids of a library by, forexample, ligating adapters comprising the index tag sequence to ends ofthe polynucleic acids.

The adapters may contain sequences in addition to the index tagsequence, such as a universal extension primer sequence and a universalsequencing primer sequence. The universal extension primer sequence may,among other things, hybridize to a first oligonucleotide coupled to asolid surface. The first oligonucleotide may have a free 3′ end fromwhich a polymerase may add nucleotides to extend the sequence using thehybridized library polynucleotide as a template, resulting in a reversestrand of the library polynucleotide being coupled to the solid surface.Additional copies of forward and reverse strands may be coupled to thesolid surface through cluster amplification. One example of clusteramplification is bridge amplification in which the 3′ end of previouslyamplified polynucleotides that are bound to the solid surface hybridizeto second oligonucleotides bound to the solid surface. The secondoligonucleotide may have a free 3′ end from which a polymerase may addnucleotides to extend the sequence using the coupled reverse strandpolynucleotide as a template, resulting in a forward strand of thelibrary polynucleotide being coupled to the solid surface via the secondoligonucleotide. The process may be repeated to produce clusters offorward and reverse strands coupled to the solid surface. The forwardstrands or the reverse strands may be removed, e.g. via cleavage, priorto sequencing.

A sequencing primer may hybridize to a portion of a polynucleotidestrand coupled to the solid support. For example, the sequencing primermay hybridize to a universal sequencing primer sequence, if present.Sequencing may occur through multiple rounds of addition of nucleotidesto the sequencing primer using the coupled polynucleotide as a template,and detecting the identity of the added nucleotides. Hybridization ofthe sequencing primer may occur at a location on the coupledpolynucleotide strand to allow sequence identification of the index tagsequence as well as a target sequence of the polynucleotide coupled tothe solid surface or separate sequencing primers may be employed toseparately sequence the index tag sequence and the target sequence.Accordingly, the target sequence may be indexed to a particular libraryof origin based on the index tag sequence associated with the targetsequence.

Despite the inclusion of a library-specific index tag sequence to eachpolynucleic acid to be sequenced, errors in identifying the libraryorigin of a sequenced polynucleic acid may occur due to a phenomenonknown as index hopping. Index hopping occurs when index tag sequencesfrom one library are inadvertently added to a polynucleic acid from adifferent library. Index hopping may occur during library preparation orcluster amplification of the polynucleotides on a flow cell or othersuitable solid support for sequencing. Index hopping may confoundresults of sequencing, such as resulting in improper assignment oflibrary origin of a sequenced polynucleotide or discarding sequencingresults.

BRIEF SUMMARY

One or more aspects of the present disclosure address at least onepotential mechanism associated with index hopping by blocking 3′ ends ofpolynucleic acids, including unincorporated adapters, during librarysample preparation. Without intending to be bound by theory, it isbelieved that index hopping may occur when an unincorporated adaptercomprising an index tag sequence for one library hybridizes to a portionof an adapter from another library, and the unincorporated adapterserves as a primer during cluster amplification. Thus, a target sequencefrom one library may be tagged with an index tag of an adapter fromanother library. During subsequent rounds of cluster amplification,additional copies of the miss-tagged target may be amplified prior tosequencing. Such index hopping may confound results of subsequentsequencing. By blocking the 3′ ends of polynucleotides in a library,including unincorporated adapters, during library sample preparation,the ability of the unincorporated adapters to serve as primers duringcluster amplification will be blocked.

In addition or alternatively, aspects of embodiments of the presentdisclosure relates to protecting from exonucleases the 5′ and 3′ ends oftemplate polynucleotides for immobilizing on a surface for sequencing,and degrading residual unprotected polynucleotides to inhibit theability of the unprotected polynucleotides from participating in indexhopping.

In some aspects described herein, a method includes providing a firstlibrary comprising a first plurality of polynucleotides having a firstadapter-target-first adapter sequence. The polynucleotides of the firstplurality of polynucleotide are double stranded in a region comprisingthe target and at least a portion of the first adapter on both ends ofthe target. The method further includes providing a first primeroligonucleotide configured to hybridize with a portion of the firstadapter in proximity to a 3′ end of a strand of the first adapter. The5′ end of the first primer oligonucleotide is modified to preventdigestion by an enzyme having 5′ exonuclease activity. The methodfurther includes providing a second primer oligonucleotide configured tohybridize with a complement of a portion of the first adapter inproximity to a 3′ end of a strand of the complement of the firstadapter. The 5′ end of the second primer oligonucleotide is modified toprevent digestion by an enzyme having 5′ exonuclease activity. Themethod further includes incubating the first library with the first andsecond primer oligonucleotides in a solution under conditions suitableto amplify the polynucleotides having a first adapter-target-firstadapter sequence to produce an amplified first library ofpolynucleotides having 5′ ends modified to prevent digestion by anenzyme having 5′ exonuclease activity. The amplified polynucleotideshave an amplified first adapter-target-amplified first adapter sequence.The amplified first adapter sequence comprises a first library-specificsequence. The method further includes modifying 3′ ends of the amplifiedfirst library polynucleotides to prevent one or both of (i) digestion byan enzyme having 3′ exonuclease activity, or (ii) addition ofnucleotides to the 3′ end by an enzyme having polymerase activity,thereby generating a protected first library of polynucleotides havingmodified 5′ and 3′ ends. Preferably, the 3′ ends are modified to inhibitthe addition of nucleotides to the 3′ end by an enzyme having polymeraseactivity.

The protected first library of polynucleotides having modified 5′ and 3′ends may be pooled with similar polynucleotides from other libraries andimmobilized for a surface for sequencing. When the 3′ ends were modifiedto include dideoxynucleotides, a decrease in index hopping of nearly100-fold was observed.

In some aspects described herein, a polynucleotide prepared forimmobilizing for sequencing has an adapter-target-adapter sequence. Theadapter sequence comprises a library specific sequence. Thepolynucleotide is double stranded in a region comprising the target andat least a portion of the adapter on both ends of the target. The, 5′and 3′ ends of the polynucleotide in a region of the adapter sequenceare single stranded. The 5′ ends are modified to prevent digestion by anenzyme having 5′ exonuclease activity. The 3′ ends are modified toinhibit one or both of (i) digestion by an enzyme having 3′ exonucleaseactivity, or (ii) addition of nucleotides to the 3′ end by an enzymehaving polymerase activity. Preferably, the 3′ ends are modified toinhibit the addition of nucleotides to the 3′ end by an enzyme havingpolymerase activity.

In some embodiments, compositions comprise the polynucleotide and anexonuclease.

The methods, polynucleotides and compositions described herein may beuseful in mitigating index hopping, for example by blocking 3′ ends ofpolynucleotides, including unincorporated adapters, or degradingunblocked polynucleotides, including unincorporated adapters, duringlibrary sample preparation. By blocking the 3′ ends of theunincorporated adapters, the unincorporated adapters cannot be extendedduring cluster amplification if the adapters hybridize to anadapter-target-adapter polynucleotide sequence during clusteramplification. In addition or alternatively, those polynucleotides thatare not blocked at the 3′ end may be degraded by an exonuclease tomitigate index hopping.

Additional features and advantages of the subject matter of the presentdisclosure will be set forth in the detailed description which follows,and in part will be readily apparent to those skilled in the art fromthat description or recognized by practicing the subject matter of thepresent disclosure as described herein, including the detaileddescription which follows, the claims, as well as the appended drawings.

It is to be understood that both the foregoing general description andthe following detailed description present embodiments of the subjectmatter of the present disclosure, and are intended to provide anoverview or framework for understanding the nature and character of thesubject matter of the present disclosure as it is claimed. Theaccompanying drawings are included to provide a further understanding ofthe subject matter of the present disclosure, and are incorporated intoand constitute a part of this specification. The drawings illustratevarious embodiments of the subject matter of the present disclosure andtogether with the description serve to explain the principles andoperations of the subject matter of the present disclosure.Additionally, the drawings and descriptions are meant to be merelyillustrative, and are not intended to limit the scope of the claims inany manner.

BRIEF DESCRIPTION OF THE DRAWINGS

The following detailed description of specific embodiments of thepresent disclosure may be best understood when read in conjunction withthe following drawings.

FIG. 1 is a schematic drawing illustrating an embodiment of a processfor producing 5′ modified and 3′ blocked template polynucleotides.

FIG. 2 is a schematic drawing of an embodiment of an adapter accordingto various aspects of the disclosure presented herein.

FIG. 3 is a schematic drawing of an embodiment of a templatepolynucleotide having an adapter-target-adapter sequence (which mayinclude an adapter generally as shown in FIG. 2) according to variousaspects of the disclosure presented herein.

FIG. 4 is a schematic drawing illustrating an embodiment of a processfor cluster amplification employing an embodiment of a templatepolynucleotide (which may be the template polynucleotide depicted inFIG. 3) according to various aspects of the disclosure presented herein.

FIG. 5 is a schematic drawing illustrating an embodiment of how 3′ endblocking may mitigate index hopping.

FIG. 6 is a schematic drawing illustrating an embodiment of howexonuclease treatment may mitigate index hopping in accordance withvarious embodiments described herein.

FIGS. 7A and 7B illustrate the nature of the index hopping phenomenon.FIG. 7A shows how reads from a given sample are incorrectlydemultiplexed and mixed with a different sample followingdemultiplexing. FIG. 7B demonstrates index hopping in a dual indexsystem, where it leads to unexpected combinations of index tagsequences.

FIGS. 8A and 8B illustrate the general approach to measuring the rate ofindex hopping in a given system. FIG. 8A shows an exemplary layout of adual adapter plate, wherein each individual well of a 96-well platecontains a unique pair of index tag sequences. FIG. 8B shows anexperimental setup aimed at measuring the rate of index hopping, whereinonly unique dual index tag combinations are used.

FIGS. 9A and 9B illustrate the effect of unligated adapters on the rateof index hopping. FIG. 9A shows a 6-fold increase in index hoppingassociated with a 50% spike-in of free adapters. FIG. 9B shows anapproximately linear effect of the free forked adapter on the rate ofindex hopping within the range tested.

FIG. 10 shows the effect of combined exonuclease and 3′ blockingtreatment on the rates of index hopping in Illumina TruSeq® Nano (PCR)library preparation work flow, comparing the performance of standardadapters and PCR-protected adapters according to the present invention.

The schematic drawings are not necessarily to scale. Like numbers usedin the figures refer to like components, steps and the like. However, itwill be understood that the use of a number to refer to a component in agiven figure is not intended to limit the component in another figurelabeled with the same number. In addition, the use of different numbersto refer to components is not intended to indicate that the differentnumbered components cannot be the same or similar to other numberedcomponents.

DETAILED DESCRIPTION

Reference will now be made in greater detail to various embodiments ofthe subject matter of the present disclosure, some embodiments of whichare illustrated in the accompanying drawings.

Definitions

All scientific and technical terms used herein have meanings commonlyused in the art unless otherwise specified. The definitions providedherein are to facilitate understanding of certain terms used frequentlyherein and are not meant to limit the scope of the present disclosure.

As used herein, singular forms “a,” “an” and “the” include pluralreferents unless the context clearly dictates otherwise. Thus, forexample, reference to an “index tag sequence” includes examples havingtwo or more such “index tag sequences” unless the context clearlyindicates otherwise.

As used in this specification and the appended claims, the term “or” isgenerally employed in its sense including “and/or” unless the contentclearly dictates otherwise. The term “and/or” means one or all of thelisted elements or a combination of any two or more of the listedelements. The use of “and/or” in some instances does not imply that theuse of “or” in other instances may not mean “and/or.”

As used herein, “have”, “has”, “having”, “include”, “includes”,“including”, “comprise”, “comprises”, “comprising” or the like are usedin their open ended inclusive sense, and generally mean “include, butnot limited to”, “includes, but not limited to”, or “including, but notlimited to”.

“Optional” or “optionally” means that the subsequently described event,circumstance, or component, can or cannot occur, and that thedescription includes instances where the event, circumstance, orcomponent, occurs and instances where it does not.

The words “preferred” and “preferably” refer to embodiments of thedisclosure that may afford certain benefits, under certaincircumstances. However, other embodiments may also be preferred, underthe same or other circumstances. Furthermore, the recitation of one ormore preferred embodiments does not imply that other embodiments are notuseful, and is not intended to exclude other embodiments from the scopeof the inventive technology.

Also herein, the recitations of numerical ranges by endpoints includeall numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2,2.75, 3, 3.80, 4, 5, etc.). Where a range of values is “greater than”,“less than”, etc. a particular value, that value is included within therange.

Unless otherwise expressly stated, it is in no way intended that anymethod set forth herein be construed as requiring that its steps beperformed in a specific order. Accordingly, where a method claim doesnot actually recite an order to be followed by its steps or it is nototherwise specifically stated in the claims or descriptions that thesteps are to be limited to a specific order, it is no way intended thatany particular order be inferred. Any recited single or multiple featureor aspect in any one claim may be combined or permuted with any otherrecited feature or aspect in any other claim or claims.

While various features, elements or steps of particular embodiments maybe disclosed using the transitional phrase “comprising,” it is to beunderstood that alternative embodiments, including those that may bedescribed using the transitional phrases “consisting” or “consistingessentially of,” are implied. Thus, for example, implied alternativeembodiments to a polynucleotide comprising an adapter-target-adaptersequence includes embodiments where the polynucleotide consists of theadapter-target-adapter sequence and embodiments where the polynucleotideconsists essentially of the adapter-target-adapter sequence.

As used herein, “providing” in the context of a polynucleotide,composition or article means making the polynucleotide, composition, orarticle, purchasing the polynucleotide, composition or article, orotherwise obtaining the compound, composition or article.

As used herein, “amplify”, “amplifying” or “amplification reaction” andtheir derivatives, refer generally to any action or process whereby atleast a portion of a polynucleotide (e.g., template polynucleotide) isreplicated or copied into at least one additional polynucleotide. Theadditional polynucleotide optionally includes a sequence that issubstantially identical or substantially complementary to at least someportion of the template polynucleotide. The template polynucleotide maybe single-stranded or double-stranded and the additional polynucleotidemay independently be single-stranded or double-stranded. Amplificationoptionally includes linear or exponential replication of apolynucleotide. In some embodiments, such amplification may be performedusing isothermal conditions; in other embodiments, such amplificationmay include thermocycling. In some embodiments, the amplification is amultiplex amplification that includes the simultaneous amplification ofa plurality of target sequences in a single amplification reaction. Insome embodiments, “amplification” includes amplification of at leastsome portion of DNA and RNA based nucleic acids alone, or incombination. The amplification reaction may include any of theamplification processes known to one of ordinary skill in the art. Insome embodiments, the amplification reaction includes polymerase chainreaction (PCR).

As used herein, the term “polymerase” is intended to be consistent withits use in the art and includes, for example, an enzyme that produces acomplementary replicate of a polynucleotide using the polynucleotide asa template strand. Typically, DNA polymerases bind to the templatestrand and then move down the template strand sequentially addingnucleotides to the free hydroxyl group at the 3′ end of a growing strandof nucleic acid. DNA polymerases typically synthesize complementary DNAmolecules from DNA templates and RNA polymerases typically synthesizeRNA molecules from DNA templates (transcription). Polymerases may use ashort RNA or DNA strand, called a primer, to begin strand growth. Somepolymerases may displace the strand upstream of the site where they areadding bases to a chain. Such polymerases are said to be stranddisplacing, meaning they have an activity that removes a complementarystrand from a template strand being read by the polymerase. Exemplarypolymerases having strand displacing activity include, withoutlimitation, the large fragment of Bst (Bacillus stearothermophilus)polymerase, exo-Klenow polymerase or sequencing grade T7 exo-polymerase.Some polymerases degrade the strand in front of them, effectivelyreplacing it with the growing chain behind (5′ exonuclease activity).Some polymerases have an activity that degrades the strand behind them(3′ exonuclease activity). Some useful polymerases have been modified,either by mutation or otherwise, to reduce or eliminate 3′ and/or 5′exonuclease activity.

As defined herein “multiplex amplification” refers to selective andnon-random amplification of two or more target sequences within a sampleusing at least one target-specific primer. In some embodiments,multiplex amplification is performed such that some or all of the targetsequences are amplified within a single reaction vessel. The “plexy” or“plex” of a given multiplex amplification refers generally to the numberof different target-specific sequences that are amplified during thatsingle multiplex amplification. In some embodiments, the plexy may beabout 12-plex, 24-plex, 48-plex, 96-plex, 192-plex, 384-plex, 768-plex,1536-plex, 3072-plex, 6144-plex or higher. It is also possible to detectthe amplified target sequences by several different methodologies (e.g.,gel electrophoresis followed by densitometry, quantitation with abioanalyzer or quantitative PCR, hybridization with a labeled probe;incorporation of biotinylated primers followed by avidin-enzymeconjugate detection; incorporation of 32P-labeled deoxynucleotidetriphosphates into the amplified target sequence).

As used herein, the term “primer” and its derivatives refer generally toany polynucleotide that may hybridize to a target sequence of interest.Typically, the primer functions as a substrate onto which nucleotidesmay be polymerized by a polymerase; in some embodiments, however, theprimer may become incorporated into the synthesized nucleic acid strandand provide a site to which another primer may hybridize to primesynthesis of a new strand that is complementary to the synthesizednucleic acid molecule. The primer may be comprised of any combination ofnucleotides or analogs thereof. In some embodiments, the primer is asingle-stranded oligonucleotide or polynucleotide. The terms“polynucleotide” and “oligonucleotide” are used interchangeably hereinto refer to a polymeric form of nucleotides of any length, and maycomprise ribonucleotides, deoxyribonucleotides, analogs thereof, ormixtures thereof. This term refers only to the primary structure of themolecule. Thus, the term includes triple-, double- and single-strandeddeoxyribonucleic acid (“DNA”), as well as triple-, double- andsingle-stranded ribonucleic acid (“RNA”). As used herein, “amplifiedtarget sequences” and its derivatives, refers generally to apolynucleotide sequence produced by the amplifying the target sequencesusing target-specific primers and the methods provided herein. Theamplified target sequences may be either of the same sense (i.e thepositive strand) or antisense (i.e., the negative strand) with respectto the target sequences.

As used herein, the terms “ligating”, “ligation” and their derivativesrefer generally to the process for covalently linking two or moremolecules together, for example covalently linking two or morepolynucleotides to each other. In some embodiments, ligation includesjoining nicks between adjacent nucleotides of polynucleotides. In someembodiments, ligation includes forming a covalent bond between an end ofa first and an end of a second polynucleotide. In some embodiments, theligation may include forming a covalent bond between a 5′ phosphategroup of one nucleic acid and a 3′ hydroxyl group of a second nucleicacid thereby forming a ligated polynucleotide.

Generally for the purposes of this disclosure, an amplified targetsequence may be ligated to an adapter to generate an adapter-ligatedamplified target sequence.

As used herein, “ligase” and its derivatives, refers generally to anyagent capable of catalyzing the ligation of two substrate molecules. Insome embodiments, the ligase includes an enzyme capable of catalyzingthe joining of nicks between adjacent nucleotides of a nucleic acid. Insome embodiments, the ligase includes an enzyme capable of catalyzingthe formation of a covalent bond between a 5′ phosphate of one nucleicacid molecule to a 3′ hydroxyl of another nucleic acid molecule therebyforming a ligated nucleic acid molecule. Suitable ligases may include,but not limited to, T4 DNA ligase, T4 RNA ligase, and E. coli DNAligase.

As used herein, “ligation conditions” and its derivatives, generallyrefers to conditions suitable for ligating two molecules to each other.In some embodiments, the ligation conditions are suitable for sealingnicks or gaps between nucleic acids. As used herein, the term nick orgap is consistent with the use of the term in the art. Typically, a nickor gap may be ligated in the presence of an enzyme, such as ligase at anappropriate temperature and pH. In some embodiments, T4 DNA ligase mayjoin a nick between nucleic acids at a temperature of about 70-72° C.

As used herein, the term “universal sequence” refers to a region ofsequence that is common to two or more nucleic acid molecules where themolecules also have regions of sequence that differ from each other. Auniversal sequence that is present in different members of a collectionof molecules may allow capture of multiple different nucleic acids usinga population of universal capture nucleic acids that are complementaryto the universal sequence. Similarly, a universal sequence present indifferent members of a collection of molecules may allow the replicationor amplification of multiple different nucleic acids using a populationof universal primers that are complementary to the universal sequence.Thus a universal capture polynucleotide or a universal primer includes asequence that may hybridize specifically to a universal sequence.Polynucleotides may be modified to attach universal adapters, forexample, at one or both ends of the different sequences.

Index Hopping

This disclosure relates to, among other things, sequencing of nucleicacids from multiple indexed libraries; and more particularly toincreasing the likelihood that sequencing properly identifies thelibrary from which the nucleic acids originated.

When polynucleotides from different libraries are pooled or multiplexedfor sequencing, the polynucleotides from each library may be modified toinclude a library-specific index tag sequence. During sequencing theindex tag is sequenced along with target polynucleotide sequences fromthe libraries. Accordingly, the index tag sequence may be associatedwith target polynucleotide sequence so that the library from which thetarget sequence originated may be identified.

However, a phenomenon referred to as index hopping may occur in a smallpercentage of sequence results (typically 0.5% to 2%). Index hoppingrefers to an index tag sequence from one library being associated withtarget polynucleotide from another library (see FIGS. 7A and 7B). Whilethe mechanisms by which index hopping may occur are not fullyunderstood, the rate of index hopping may be effectively reduced byblocking the 3′ end of unincorporated adapters after the adapters areattached to the target polynucleotides of a library to, among otherthings, attach the index tag sequence to the polynucleotide.

Initial Library Sample Preparation

Libraries comprising polynucleotides may be prepared in any suitablemanner to attach oligonucleotide adapters to target polynucleotides. Asused herein, a “library” is a population of polynucleotides from a givensource or sample. A library comprises a plurality of targetpolynucleotides. As used herein, a “target polynucleotide” is apolynucleotide that is desired to sequence. The target polynucleotidemay be essentially any polynucleotide of known or unknown sequence. Itmay be, for example, a fragment of genomic DNA or cDNA. Sequencing mayresult in determination of the sequence of the whole, or a part of thetarget polynucleotides. The target polynucleotides may be derived from aprimary polynucleotide sample that has been randomly fragmented. Thetarget polynucleotides may be processed into templates suitable foramplification by the placement of universal primer sequences at the endsof each target fragment. The target polynucleotides may also be obtainedfrom a primary RNA sample by reverse transcription into cDNA.

The terms “polynucleotide” and “oligonucleotide” are usedinterchangeably herein to refer to a polymeric form of nucleotides ofany length, and may comprise ribonucleotides, deoxyribonucleotides,analogs thereof, or mixtures thereof. This term refers only to theprimary structure of the molecule. Thus, the term includes triple-,double- and single-stranded deoxyribonucleic acid (“DNA”), as well astriple-, double- and single-stranded ribonucleic acid (“RNA”). The termspolynucleotide and oligonucleotide used herein also encompasses cDNA,that is complementary or copy DNA produced from an RNA template, forexample by the action of reverse transcriptase.

Primary polynucleotide molecules may originate in double-stranded DNA(dsDNA) form (e.g. genomic DNA fragments, PCR and amplification productsand the like) or may have originated in single-stranded form, as DNA orRNA, and been converted to dsDNA form. By way of example, mRNA moleculesmay be copied into double-stranded cDNAs using standard techniques wellknown in the art. The precise sequence of primary polynucleotides isgenerally not material to the disclosure presented herein, and may beknown or unknown.

In some embodiments, the primary target polynucleotides are RNAmolecules. In an aspect of such embodiments, RNA isolated from specificsamples is first converted to double-stranded DNA using techniques knownin the art. The double-stranded DNA may then be index tagged with alibrary specific tag. Different preparations of such double-stranded DNAcomprising library specific index tags may be generated, in parallel,from RNA isolated from different sources or samples. Subsequently,different preparations of double-stranded DNA comprising differentlibrary specific index tags may be mixed, sequenced en masse, and theidentity of each sequenced fragment determined with respect to thelibrary from which it was isolated/derived by virtue of the presence ofa library specific index tag sequence.

In some embodiments, the primary target polynucleotides are DNAmolecules. For example, the primary polynucleotides may represent theentire genetic complement of an organism, and are genomic DNA molecules,such as human DNA molecules, which include both intron and exonsequences (coding sequence), as well as non-coding regulatory sequencessuch as promoter and enhancer sequences. Although it could be envisagedthat particular sub-sets of polynucleotide sequences or genomic DNAcould also be used, such as, for example, particular chromosomes or aportion thereof. In many embodiments, the sequence of the primarypolynucleotides is not known. The DNA target polynucleotides may betreated chemically or enzymatically either prior to, or subsequent to afragmentation processes, such as a random fragmentation process, andprior to, during, or subsequent to the ligation of the adaptoroligonucleotides.

Preferably, the primary target polynucleotides are fragmented toappropriate lengths suitable for sequencing. The target polynucleotidesmay be fragmented in any suitable manner. Preferably, the targetpolynucleotides are randomly fragmented. Random fragmentation refers tothe fragmentation of a polynucleotide in a non-ordered fashion by, forexample, enzymatic, chemical or mechanical means. Such fragmentationmethods are known in the art and utilize standard methods (Sambrook andRussell, Molecular Cloning, A Laboratory Manual, third edition). For thesake of clarity, generating smaller fragments of a larger piece ofpolynucleotide via specific PCR amplification of such smaller fragmentsis not equivalent to fragmenting the larger piece of polynucleotidebecause the larger piece of polynucleotide remains in intact (i.e., isnot fragmented by the PCR amplification). Moreover, random fragmentationis designed to produce fragments irrespective of the sequence identityor position of nucleotides comprising and/or surrounding the break.

In some embodiments, the random fragmentation is by mechanical meanssuch as nebulization or sonication to produce fragments of about 50 basepairs in length to about 1500 base pairs in length, such as 50-700 basepairs in length or 50-500 base pairs in length.

Fragmentation of polynucleotide molecules by mechanical means(nebulization, sonication and Hydroshear for example) may result infragments with a heterogeneous mix of blunt and 3′- and 5′-overhangingends. Fragment ends may be repaired using methods or kits (such as theLucigen DNA terminator End Repair Kit) known in the art to generate endsthat are optimal for insertion, for example, into blunt sites of cloningvectors. In some embodiments, the fragment ends of the population ofnucleic acids are blunt ended. The fragment ends may be blunt ended andphosphorylated. The phosphate moiety may be introduced via enzymatictreatment, for example, using polynucleotide kinase.

In some embodiments, the target polynucleotide sequences are preparedwith single overhanging nucleotides by, for example, activity of certaintypes of DNA polymerase such as Taq polymerase or Klenow exo minuspolymerase which has a non-template-dependent terminal transferaseactivity that adds a single deoxynucleotide, for example, deoxyadenosine(A) to the 3′ ends of, for example, PCR products. Such enzymes may beutilized to add a single nucleotide ‘A’ to the blunt ended 3′ terminusof each strand of the target polynucleotide duplexes. Thus, an ‘ A’could be added to the 3′ terminus of each end repaired duplex strand ofthe target polynucleotide duplex by reaction with Taq or Klenow exominus polymerase, while the adaptor polynucleotide construct could be aT-construct with a compatible ‘ T overhang present on the 3’ terminus ofeach duplex region of the adapter construct. This end modification alsoprevents self-ligation of the target polynucleotides such that there isa bias towards formation of the combined ligated adapter-targetpolynucleotides.

In some embodiments, fragmentation is accomplished through tagmentationas described in, for example, International Patent ApplicationPublication WO 2016/130704. In such methods transposases are employed tofragment a double stranded polynucleotide and attach a universal primersequence into one strand of the double stranded polynucleotide. Theresulting molecule may be gap-filled and subject to extension, forexample by PCR amplification, using primers that comprise a 3′ end thathybridizes to the attached universal primer sequence and a 5′ end thatcontains other sequences of an adapter or using primers that comprise a3′ end that hybridizes to a complement of the attached universal primersequence and a 5′ end that contains other sequences of an adapter.

The adapters or portions of the adapters may be attached to the targetpolynucleotide in any other suitable manner. In some embodiments, theadapters are introduced in a multi-step process, such as a two-stepprocess, involving ligation of a portion of the adapter to the targetpolynucleotide having a universal primer sequence. The second stepcomprises extension, for example by PCR amplification, using primersthat comprise a 3′ end that hybridizes to the attached universal primersequence (or that hybridizes to a complement of the universal primersequence) and a 5′ end that contains other sequences of an adapter. Byway of example, such extension may be performed as described in U.S.Pat. No. 8,053,192. Additional extensions may be performed to provideadditional sequences to the 5′ end of the resulting previously extendedpolynucleotide.

In some embodiments, the entire adapter is ligated to the fragmentedtarget polynucleotide. The ligated adapter comprises a double strandedregion that is ligated to a double stranded target polynucleotide.Preferably, the double-stranded region is as short as possible withoutloss of function. In this context, “function” refers to the ability ofthe double-stranded region to form a stable duplex under standardreaction conditions. In some embodiments, standard reactions conditionsrefer to reaction conditions for an enzyme-catalyzed polynucleotideligation reaction, which will be well known to the skilled reader (e.g.incubation at a temperature in the range of 4° C. to 25° C. in aligation buffer appropriate for the enzyme), such that the two strandsforming the adaptor remain partially annealed during ligation of theadaptor to a target molecule. Ligation methods are known in the art andmay utilize standard methods (Sambrook and Russell, Molecular Cloning, ALaboratory Manual, third edition). Such methods utilize ligase enzymessuch as DNA ligase to effect or catalyze joining of the ends of the twopolynucleotide strands of, in this case, the adapter duplexoligonucleotide and the target polynucleotide duplexes, such thatcovalent linkages are formed. The adaptor duplex oligonucleotide maycontain a 5′-phosphate moiety in order to facilitate ligation to atarget polynucleotide 3′-OH. The target polynucleotide may contain a5′-phosphate moiety, either residual from the shearing process, or addedusing an enzymatic treatment step, and has been end repaired, andoptionally extended by an overhanging base or bases, to give a 3′-OHsuitable for ligation. In this context, attaching means covalent linkageof polynucleotide strands which were not previously covalently linked.In a particular aspect of the invention, such attaching takes place byformation of a phosphodiester linkage between the two polynucleotidestrands, but other means of covalent linkage (e.g. non-phosphodiesterbackbone linkages) may be used. Ligation of adapters to targetpolynucleotides is described in more detail in, for example, U.S. Pat.No. 8,053,192.

Whether the entire adapter or a portion of the adapter is attached tothe double stranded target fragment, the adapter or portion comprises adouble stranded region and a region comprising two non-complementarysingle strands. The double-stranded region of the adapter may be of anysuitable number of base pairs. Preferably, the double stranded region isa short double-stranded region, typically comprising 5 or moreconsecutive base pairs, formed by annealing of two partiallycomplementary polynucleotide strands. This “double-stranded region” ofthe adapter refers to a region in which the two strands are annealed anddoes not imply any particular structural conformation. In someembodiments, the double stranded region comprises 20 or less consecutivebase pairs, such as 10 or less or 5 or less consecutive base pairs.

The stability of the double-stranded region may be increased, and henceits length potentially reduced, by the inclusion of non-naturalnucleotides which exhibit stronger base-pairing than standardWatson-Crick base pairs. Preferably, the two strands of the adaptor are100% complementary in the double-stranded region.

When the adapter is attached to the target polynucleotide, thenon-complementary single stranded region may form the 5′ and 3′ ends ofthe polynucleotide to be sequenced. The term “non-complementary singlestranded region” refers to a region of the adapter where the sequencesof the two polynucleotide strands forming the adaptor exhibit a degreeof non-complementarity such that the two strands are not capable offully annealing to each other under standard annealing conditions for aPCR reaction.

The non-complementary single stranded region is provided by differentportions of the same two polynucleotide strands which form thedouble-stranded region. The lower limit on the length of thesingle-stranded portion will typically be determined by function of, forexample, providing a suitable sequence for binding of a primer forprimer extension, PCR and/or sequencing. Theoretically there is no upperlimit on the length of the unmatched region, except that in general itis advantageous to minimize the overall length of the adaptor, forexample, in order to facilitate separation of unbound adapters fromadapter-target constructs following the attachment step or steps.Therefore, it is generally preferred that the non-complementarysingle-stranded region of the adapter is 50 or less consecutivenucleotides in length, such as 40 or less, 30 or less, or 25 or lessconsecutive nucleotides in length.

After the adapters or portions of the adapters are attached to thetarget polynucleotides, the resulting polynucleotides may be subjectedto a clean-up process to enhance the purity to theadapter-target-adapter polynucleotides by removing at least a portion ofthe unincorporated adapters. Any suitable clean-up process may be used,such as electrophoresis, size exclusion chromatography, or the like. Insome embodiments, solid phase reverse immobilization (SPRI) paramagneticbeads may be employed to separate the adapter-target-adapterpolynucleotides from the unattached adapters. While such processes mayenhance the purity of the resulting adapter-target-adapterpolynucleotides, some unattached adapter oligonucleotides likely remain.

As used herein, “attached” or “bound” are used interchangeably in thecontext of an adapter relative to a target sequence. As described above,any suitable process may be used to attach an adapter to a targetpolynucleotide. For example, the adapter may be attached to the targetthrough ligation with a ligase; through a combination of ligation of aportion of an adapter and addition of further or remaining portions ofthe adapter through extension, such as PCR, with primers containing thefurther or remaining portions of the adapters; trough transposition toincorporate a portion of an adapter and addition of further or remainingportions of the adapter through extension, such as PCR, with primerscontaining the further or remaining portions of the adapters; or thelike. Preferably, the attached adapter oligonucleotide is covalentlybound to the target polynucleotide.

Amplification

The polynucleotide resulting from attaching the adapter or portion ofthe adapter to the double stranded target is then subjected toamplification with primers having 5′ ends that are modified to preventdigestion by an enzyme having 5′ exonuclease activity.

The 5′ ends of the primers may be modified in any suitable manner toprevent digestion by an enzyme having 5′ exonuclease activity. Forpurposes of the present disclosure, a modification that “prevents”digestion by an exonuclease inhibits the activity of the exonucleaserelative to its action on an unmodified end. Preferably, a modificationthat prevents digestion exonuclease eliminates the ability of theexonuclease to digest the polynucleotide strand. In some embodiments,the 5′ ends of the primers comprise a phosphorothioate bond. Preferably,bonds between the terminal three nucleotides of the 5′ ends of theprimers comprise phosphorothioate bonds. For purpose of the presentdisclosure, an end of a polynucleotide whose bonds between the terminalthree nucleotides comprise phosphorothioate bonds may be referred to asan end comprising three phosphorothioate bonds. Phosphorothioate bondsmay be introduced into a 5′ end of a polynucleotide in any suitablemanner, as is well known in the art.

Oligonucleotides comprising terminal phosphorothioate bonds may bepurchased from a number of commercial vendors including, for example,Integrated DNA Technologies and Sigma-Aldrich.

If the adapter attached to the target prior to amplification is only aportion of the adapter, the remainder of the adapter may be provided bythe 5′ ends of the primers.

In either case, a first primer oligonucleotide for amplification thathas a modified 5′ end is configured to hybridize with a portion of theadapter or adapter portion in proximity to a 3′ end of a strand of theadapter or portion. A second primer oligonucleotide for amplificationthat has a modified 5′ end is configured to hybridize with a complementof a portion of the adapter or adapter portion in proximity to a 3′ endof a strand of the complement of the adapter or portion. A complement ofthe adapter may result from extension of the first primer using theadapter-target-adapter as a template. Once the complement is formed, thesecond adapter may hybridize to the complement.

The first and second primers may be incubated with the polynucleotideresulting from attaching the adapter or portion of the adapter to thedouble stranded target (an “adapter-target-adapter” polynucleotide)under conditions suitable to amplify the adapter-target-adapterpolynucleotides to produce polynucleotides having an amplifiedadapter-target-amplified adapter sequence with modified 5′ ends. If theadapter-target-adapter polynucleotides comprise the entire adapter, theadapter-target-adapter polynucleotides may have the same sequence as theamplified adapter-target-amplified adapter sequence. If theadapter-target-adapter polynucleotides contain only a portion of theadapter, the amplified adapter-target-amplified adapter sequence willhave additional nucleotides at the single stranded ends of the amplifiedadapter sequence due to the addition of the remainder of the adaptersequence from the primers.

As used herein, “conditions suitable for amplification” and itsderivatives, generally refers to conditions suitable for amplifying oneor more polynucleotide sequences. Such amplification may be linear orexponential. In some embodiments, the amplification conditions mayinclude isothermal conditions or alternatively may include thermocyclingconditions, or a combination of isothermal and thermocycling conditions.In some embodiments, the conditions suitable for amplifying one or morepolynucleotide sequences include polymerase chain reaction (PCR)conditions. Typically, the amplification conditions refer to a reactionmixture that is sufficient to amplify polynucleotides such as one ormore target sequences, or to amplify an amplified target sequenceligated to one or more adapters, e.g., an adapter-ligated amplifiedtarget sequence. Generally, the amplification conditions include acatalyst for amplification or for polynucleotide synthesis, for examplea polymerase; a primer that possesses some degree of complementarity tothe nucleic acid to be amplified; and nucleotides, such asdeoxyribonucleotide triphosphates (dNTPs) to promote extension of theprimer once hybridized to the nucleic acid. The amplification conditionsmay require hybridization or annealing of a primer to a nucleic acid,extension of the primer and a denaturing step in which the extendedprimer is separated from the polynucleotide sequence undergoingamplification. Typically, but not necessarily, amplification conditionsmay include thermocycling; in some embodiments, amplification conditionsinclude a plurality of cycles where the steps of annealing, extendingand separating are repeated. Typically, the amplification conditionsinclude cations such as Mg++ or Mn++ and may also include variousmodifiers of ionic strength.

As used herein, the term “polymerase chain reaction” (“PCR”) refers tothe method of K. B. Mullis U.S. Pat. Nos. 4,683,195 and 4,683,202, whichdescribe a method for increasing the concentration of a segment of apolynucleotide of interest in a mixture of genomic DNA without cloningor purification. This process for amplifying the polynucleotide ofinterest consists of introducing a large excess of two oligonucleotideprimers to the DNA mixture containing the desired polynucleotide ofinterest, followed by a series of thermal cycling in the presence of aDNA polymerase. The two primers are complementary to their respectivestrands of the double stranded polynucleotide of interest. The mixtureis denatured at a higher temperature first and the primers are thenannealed to complementary sequences within the polynucleotide ofinterest molecule. Following annealing, the primers are extended with apolymerase to form a new pair of complementary strands. The steps ofdenaturation, primer annealing and polymerase extension may be repeatedmany times (referred to as thermocycling) to obtain a high concentrationof an amplified segment of the desired polynucleotide of interest. Thelength of the amplified segment of the desired polynucleotide ofinterest (amplicon) is determined by the relative positions of theprimers with respect to each other, and therefore, this length is acontrollable parameter. By virtue of repeating the process, the methodis referred to as the “polymerase chain reaction” (hereinafter “PCR”).Because the desired amplified segments of the polynucleotide of interestbecome the predominant nucleic acid sequences (in terms ofconcentration) in the mixture, they are said to be “PCR amplified”. In amodification to the method discussed above, the polynucleotides may bePCR amplified using a plurality of different primer pairs, in somecases, one or more primer pairs per polynucleotide of interest, therebyforming a multiplex PCR reaction.

Amplification of the adapter-target-adapter polynucleotides with the 5′modified primers results in a polynucleotide having amplifiedadapter-target-amplified adapter sequences with modified 5′ ends.

The resulting amplified adapter includes a library-specific index tagsequence. Accordingly, the index tag is not itself formed by part of thetarget polynucleotide, but becomes part of the template foramplification on a solid surface for sequencing.

Preferably, the index tag sequence is 20 nucleotides or less in length.For example, the index tag sequence may be 1-10 nucleotides or 4-6nucleotides in length. A four nucleotide index tag gives a possibilityof multiplexing 256 samples on the same array, a six base index tagenables 4096 samples to be processed on the same array.

The amplified adapters may contain more than one index tag so that themultiplexing possibilities may be increased.

The library-specific index tag sequence may be located in asingle-stranded, double-stranded region, or span the single-stranded anddouble-stranded regions of the adapter. Preferably, the index tagsequence is in a single-stranded region of the adapter.

The library-specific index tag sequence may be included on one or bothof the 5′ modified primers or may be included in a portion of theadapter that attached to the template fragment. If the library-specificindex tag sequence is not included in the primers but is included in theportion of the adapter that is attached to the template fragment (andthe primers add the remaining portion of the adapter),adapter-target-adapter polynucleotides from different libraries may bepooled to perform the amplification to the amplifiedadapter-target-amplified adapter polynucleotides. If the primers includethe library-specific index tag sequence, then each library should beamplified separately prior to pooling.

In any case, the amplified adapters may include any other suitablesequence in addition to the index tag sequence. For example, theamplified adapters may comprise universal extension primer sequences,which are typically located at the 5′ or 3′ end of the amplified adapterand the resulting template polynucleotide for sequencing. The universalextension primer sequences may hybridize to complementary primers boundto a surface of a solid substrate. The complementary primers comprise afree 3′ end from which a polymerase or other suitable enzyme may addnucleotides to extend the sequence using the hybridized librarypolynucleotide as a template, resulting in a reverse strand of thelibrary polynucleotide being coupled to the solid surface. Suchextension may be part of a sequencing run or cluster amplification.

In some embodiments, the amplified adapters comprise one or moreuniversal sequencing primer sequences. The universal sequencing primersequences may bind to sequencing primers to allow sequencing of an indextag sequence, a target sequence, or an index tag sequence and a targetsequence.

The precise nucleotide sequence of the amplified adapters is generallynot material to the invention and may be selected by the user such thatthe desired sequence elements are ultimately included in the commonsequences of the library of templates derived from the amplifiedadaptors to, for example, provide binding sites for particular sets ofuniversal extension primers and/or sequencing primers.

It will be understood that an “adapter-target-adapter sequence” or itsequivalents refers to the orientation of the adapters relative to oneanother and to the target and does not necessarily mean that thesequence may not include additional sequences, such as linker sequences,for example.

Other libraries may be prepared in a similar manner, each including atleast one library-specific index tag sequence or combinations of indextag sequences different than an index tag sequence or combination ofindex tag sequences from the other libraries.

A clean-up process, such as described above, may be performed on theresulting template polynucleotides having the amplifiedadapter-template-amplified adapter sequences.

The resulting adapter-target-adapter polynucleotides, whether or notfirst subjected to cleaned-up, along with any unincorporated primeroligonucleotides or remaining polynucleotides species are subjected to3′ blocking.

3′ Blocking

3′ blocking may be performed on each library separately or on pooledlibraries. Preferably, 3′ blocking is performed on pooled libraries.

3′ blocked means that polynucleotides are modified to preventincorporation of nucleotides on the 3′end to extend the polynucleotidefrom the 3′ end or to prevent digestion by an enzyme having 3′exonuclease activity. Preferably, the 3′ ends are blocked to preventincorporation of nucleotides on the 3′end to extend the polynucleotidefrom the 3′ end. More preferably, the 3′ ends are blocked to preventincorporation of nucleotides on the 3′ end to extend the polynucleotidefrom the 3′ end and to prevent digestion by an enzyme having 3′exonuclease activity.

In some embodiments, the 3′-OH blocking group may be removable, suchthat the 3′ carbon atom has attached a group of the structure —O—Z,wherein Z is any of C(R′)₂—O—R″, —C(R′)₂—N(R″)₂, —C(R′)₂—N(H)R″,—C(R′)₂—S—R″ and —C(R′)₂—F, wherein each R″ is or is part of a removableprotecting group; each R′ is independently a hydrogen atom, an alkyl,substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl,heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amidogroup, or a detectable label attached through a linking group; or (R′)₂represents an alkylidene group of formula ═C(R′″)₂ wherein each R′″ maybe the same or different and is selected from the group comprisinghydrogen and halogen atoms and alkyl groups; and wherein said moleculemay be reacted to yield an intermediate in which each R″ is exchangedfor H or, where Z is —C(R′)₂—F, the F is exchanged for OH, SH or NH₂,preferably OH, which intermediate dissociates under aqueous conditionsto afford a molecule with a free 3′OH; with the proviso that where Z is—C(R′)₂—S—R″, both R′ groups are not H. Where the blocking group is anyof —C(R′)₂—O—R″, —C(R′)₂—N(R″)₂, —C(R′)₂—N(H)R″, —C(R′)₂—S—R″ and—C(R′)₂—F, i.e. of formula Z, each R′ may be independently H or analkyl. Preferably, Z is of formula —C(R′)₂—O—R″, —C(R′)₂—N(R″)₂,—C(R′)₂—N(H)R″ and —C(R′)₂—SR″. Particularly preferably, Z is of theformula —C(R′)₂—O—R″, —C(R′)₂—N(R″)₂, and —C(R′)₂—SR″. R″ may be abenzyl group or a substituted benzyl group. One example of groups ofstructure —O—Z wherein Z is —C(R′)₂—N(R″)₂ are those in which —N(R″)₂ isazido (—N₃). One such example is azidomethyl wherein each R′ is H.Alternatively, R′ in Z groups of formula —C(R′)₂—N₃ and other Z groupsmay be any of the other groups discussed herein. Examples of typical R′groups include C₁₋₆ alkyl, particularly methyl and ethyl. Othernon-limiting examples of suitable 3′ blocking groups are provided inGreene et al., “Protective Groups in Organic Synthesis,” John Wiley &Sons, New York (1991), U.S. Pat. Nos. 5,990,300, 5,872,244, 6,232,465,6,214,987, 5,808,045, 5,763,594, 7,057,026, 7,566,537, 7,785,796,8,148,064, 8,394,586, 9,388,463, 9,410,200, 7,427,673, 7,772,384,8,158,346, 9,121,062, 7,541,444, 7,771,973, 8,071,739, 8,597,881,9,121,060, 9,388,464, 8,399,188, 8,808,988, 9,051,612, 9,469,873, andU.S. Pub. Nos. 2016/0002721 and 2016/0060692, the entire contents ofwhich are incorporated herein by reference.

3′ blocking may be accomplished in any suitable manner. For example, ablocking moiety may be covalently attached to a 3′ hydroxyl group at the3′ end to prevent extension from the 3′ end. Preferably, the blockinggroup remains covalently bound during subsequent processes associatedwith immobilizing adapter-target-adapter polynucleotides to a solidsurface and sequencing.

In some embodiments, a dideoxynucleotide (ddNTP) is incorporated ontothe 3′ end of a polynucleotide to block the 3′ end. The ddNTP may beincorporated in any suitable manner. In some embodiments, a ddNTP isincorporated via a terminal deoxynucleotidyl transferase (TdT). TdTs areable to incorporated nucleotides onto a 3′ end of single or doublestranded DNA without a template. In some embodiments, a ddNTP isincorporated onto a 3′ end via a TdT in the presence of a DNApolymerase, such as, for example, Pol19, Pol812 or Pol963 polymerase.Non-limiting examples of other suitable polymerases are provided in U.S.Pat. Nos. 8,460,910, 8,852,910, 8,623,628, 9,273,352, 9,447,389, andU.S. Pub. Nos. 2015/0376582, 2016/0032377, 2016/0090579, 2016/0115461,the entire contents of which are incorporated herein by reference.

In some embodiments, a digoxigenin-labeled dideoxyuridine triphosphateis added to the 3′ end using terminal transferase to block the 3′ end.Kits for adding digoxigenin-labeled dideoxyuridine triphosphate to a 3′end of a polynucleotide are available from, for example, Sigma-Aldrich.

Any other suitable process may also be employed to modify the 3′ ends ofthe polynucleotides.

During or following 3′ blocking a number of compounds and compositionsmay result. For example, a polynucleotide may result that has a firstadapter-target-second adapter sequence of nucleotides in which a 5′ endsof the polynucleotides are blocked and the 3′ ends of the polynucleotideis blocked. Compositions or libraries comprising the 5′ modified and 3′blocked polynucleotides may result. Pooled libraries and compositioncomprising pooled libraries of such polynucleotides may result.

By way of further example, a composition comprising such polynucleotidesand an enzyme and reagent for blocking 3′ ends of the polynucleotide mayresult. Similarly, a composition comprising a library of polynucleotidesand the enzyme and reagent may result. Compositions comprising pooledlibraries of such polynucleotides and the enzyme and reagent may result.In some embodiments, the compositions comprise a ddNTP. The compositionsmay further comprise a TdT. The compositions may further comprise a DNApolymerase, such as, for example, Pol19, Pol812 or Pol963 polymerase.

A clean-up process, such as described above, may be performed followingblocking.

Exonuclease Treatment

After (or during) blocking the resulting solutions or compositionscomprising the resulting polynucleotides, whether or not first subjectedto cleanup may, optionally, be subjected to treatment with anexonuclease. Preferably, the exonuclease treatment has 3′ exonucleaseactivity to degrade any polynucleotides that remain that are not 3′blocked. Because the 5′ ends are exonuclease resistant, the exonucleasemay have both 5′ exonuclease activity and 3′ exonuclease activity.

An exonuclease that has “5′ exonuclease activity” is an exonuclease thatdigests DNA in a 5′ to 3′ direction. An exonuclease that has “3′exonuclease activity” is an exonuclease that digests DNA in a 3′ to 5′direction.

One example of a suitable exonuclease that has both 5′ and 3′exonuclease activity is Exonuclease V, which is a RecBCD complex from E.coli and is available from, for example, New England Biolabs.Exonuclease V also has activity for double-stranded DNA without nicking.

Exonuclease treatment may be performed on each library separately or onpooled libraries. Following exonuclease treatment, a clean-up step, suchas described above, may be performed prior to immobilizing thepolynucleotides on a solid surface for sequencing.

If the libraries have not been pooled, they may be pooled prior toimmobilizing on a surface of sequencing.

Preparation of Immobilized Samples for Sequencing

The pooled 5′ modified and 3′blocked library preparations may then beimmobilized on a solid surface for in preparation for sequencing.Sequencing may be performed as an array of single molecules, or may beamplified prior to sequencing. The amplification may be carried outusing one or more immobilized primers. The immobilized primer(s) may bea lawn on a planar surface, clusters on a planar surface, in wells of amulti-well structure, on a pool of beads, or the like. The pool of beadsmay be isolated into an emulsion with a single bead in each“compartment” of the emulsion. At a concentration of only one templateper “compartment”, only a single template is amplified on each bead.

The term “solid-phase amplification” as used herein refers to anypolynucleotide amplification reaction carried out on or in associationwith a solid support such that all or a portion of the amplifiedproducts are immobilized on the solid support as they are formed. Inparticular, the term encompasses solid-phase polymerase chain reaction(solid-phase PCR) and solid phase isothermal amplification which arereactions analogous to standard solution phase amplification, exceptthat one or both of the forward and reverse amplification primers is/areimmobilized on the solid support. Solid phase PCR covers systems such asemulsions, wherein one primer is anchored to a bead and the other is infree solution, and colony formation in solid phase gel matrices whereinone primer is anchored to the surface, and one is in free solution.

Although the disclosure encompasses “solid-phase” amplification methodsin which only one amplification primer is immobilized (the other primerusually being present in free solution), it is preferred for the solidsupport to be provided with both the forward and the reverse primersimmobilized. In practice, there will be a “plurality” of identicalforward primers and/or a “plurality” of identical reverse primersimmobilized on the solid support, since the amplification processrequires an excess of primers to sustain amplification. Referencesherein to forward and reverse primers are to be interpreted accordinglyas encompassing a “plurality” of such primers unless the contextindicates otherwise.

As will be appreciated by the skilled reader, any given amplificationreaction requires at least one type of forward primer and at least onetype of reverse primer specific for the template to be amplified.However, in certain embodiments the forward and reverse primers maycomprise template-specific portions of identical sequence, and may haveentirely identical nucleotide sequence and structure (including anynon-nucleotide modifications). In other words, it is possible to carryout solid-phase amplification using only one type of primer, and suchsingle-primer methods are encompassed within the scope of the invention.Other embodiments may use forward and reverse primers which containidentical template-specific sequences but which differ in some otherstructural features. For example one type of primer may contain anon-nucleotide modification which is not present in the other.

Throughout this disclosure, the terms “P5” and “P7” are used whenreferring to adapters and/or amplification primers. It will beunderstood that any suitable amplification primers can be used in themethods presented herein, and that the use of P5 and P7 are exemplaryembodiments only. Uses of amplification primers such as P5 and P7 onflowcells is known in the art, as exemplified by the disclosures of WO2007/010251, WO 2006/064199, WO 2005/065814, WO 2015/106941, WO1998/044151, and WO 2000/018957, each of which is incorporated byreference in its entirety. For example, any suitable forwardamplification primer, whether immobilized or in solution, can be usefulin the methods presented herein for hybridization to a complementarysequence and amplification of a sequence. Similarly, any suitablereverse amplification primer, whether immobilized or in solution, can beuseful in the methods presented herein for hybridization to acomplementary sequence and amplification of a sequence. One of skill inthe art will understand how to design and use primer sequences that aresuitable for capture, and amplification of nucleic acids as presentedherein.

Primers for solid-phase amplification are preferably immobilized bysingle point covalent attachment to the solid support at or near the 5′end of the primer, leaving the template-specific portion of the primerfree to anneal to its cognate template and the 3′ hydroxyl group freefor primer extension. Any suitable covalent attachment means known inthe art may be used for this purpose. The chosen attachment chemistrywill depend on the nature of the solid support, and any derivatizationor functionalization applied to it. The primer itself may include amoiety, which may be a non-nucleotide chemical modification, tofacilitate attachment. In some embodiments, the primer includes includea sulfur-containing nucleophile, such as phosphorothioate orthiophosphate, at the 5′ end. The surface of the solid support mayinclude or be modified to include a moiety to which thesulfur-containing nucleophile may attach. For example, asulfur-containing nucleophile may bind to a bromoacetamide group. Insome embodiments a solid-supported polyacrylamide hydrogel comprises abromoacetamide group for binding a sulfur-containing nucleophile. A moreparticular means of attaching primers and templates to a solid supportis via 5′ phosphorothioate attachment to a hydrogel comprised ofpolymerized acrylamide and N-(5-bromoacetamidylpentyl) acrylamide(BRAPA), as described fully in WO 2005/065814.

Solid supports comprised of an inert substrate or matrix (e.g. glassslides, polymer beads, etc) may be “functionalized”, for example byapplication of a layer or coating of an intermediate material comprisingreactive groups which permit covalent attachment to biomolecules, suchas polynucleotides. Examples of such supports include, but are notlimited to, polyacrylamide hydrogels supported on an inert substratesuch as glass. In such embodiments, the biomolecules (e.g.polynucleotides) may be directly covalently attached to the intermediatematerial (e.g. the hydrogel), but the intermediate material may itselfbe non-covalently attached to the substrate or matrix (e.g. the glasssubstrate). The term “covalent attachment to a solid support” is to beinterpreted accordingly as encompassing this type of arrangement.

The pooled library samples may be amplified on a solid surface containsa forward and reverse amplification primer. In some embodiments, thepooled libraries of polynucleotides are used to prepare clustered arraysof polynucleic acid colonies, analogous to those described in U.S. Pat.Pub. No. 2005/0100900, U.S. Pat. No. 7,115,400, WO 00/18957 and WO98/44151, by solid-phase amplification and more particularly solid phaseisothermal amplification. The terms “cluster” and “colony” are usedinterchangeably herein to refer to a discrete site on a solid supportcomprised of a plurality of identical immobilized nucleic acid strandsand a plurality of identical immobilized complementary nucleic acidstrands. The term “clustered array” refers to an array formed from suchclusters or colonies. In this context the term “array” is not to beunderstood as requiring an ordered arrangement of clusters.

The term solid phase, or surface, is used to mean either a planar arraywherein primers are attached to a flat surface, for example, glass,silica or plastic microscope slides or similar flow cell devices; beads,wherein either one or two primers are attached to the beads and thebeads are amplified; an array of beads on a surface after the beads havebeen amplified; or the like.

The terms “solid surface,” “solid support” and other grammaticalequivalents herein refer to any material that is appropriate for or maybe modified to be appropriate for the attachment of the templatepolynucleotides. As will be appreciated by those in the art, the numberof possible substrates is very large. Possible substrates include, butare not limited to, glass and modified or functionalized glass, plastics(including acrylics, polystyrene and copolymers of styrene and othermaterials, polypropylene, polyethylene, polybutylene, polyurethanes,Teflon®, etc.), polysaccharides, nylon or nitrocellulose, ceramics,resins, silica or silica-based materials including silicon and modifiedsilicon, carbon, metals, inorganic glasses, plastics, optical fiberbundles, and a variety of other polymers. Particularly useful solidsupports and solid surfaces for some embodiments are located within aflow cell apparatus. Exemplary flow cells are set forth in furtherdetail below.

In some embodiments, the solid support comprises a patterned surface. A“patterned surface” refers to an arrangement of different regions in oron an exposed layer of a solid support. For example, one or more of theregions may be features where one or more amplification primers arepresent. The features may be separated by interstitial regions whereamplification primers are not present. In some embodiments, the patternmay be an x-y format of features that are in rows and columns. In someembodiments, the pattern may be a repeating arrangement of featuresand/or interstitial regions. In some embodiments, the pattern may be arandom arrangement of features and/or interstitial regions. Exemplarypatterned surfaces that may be used in the methods and compositions setforth herein are described in U.S. Pat. Nos. 8,778,848, 8,778,849,9,079,148, and U.S. Pub. No. 2014/0243224.

In some embodiments, the solid support comprises an array of wells ordepressions in a surface. This may be fabricated as is generally knownin the art using a variety of techniques, including, but not limited to,photolithography, stamping techniques, molding techniques andmicroetching techniques. As will be appreciated by those in the art, thetechnique used will depend on the composition and shape of the arraysubstrate.

The features in a patterned surface may be wells in an array of wells(e.g. microwells or nanowells) on glass, silicon, plastic or othersuitable solid supports with patterned, covalently-linked gel such aspoly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM, see,for example, U.S. Pub. No. 2013/184796, WO 2016/066586, and WO2015/002813). The process creates gel pads used for sequencing that maybe stable over sequencing runs with a large number of cycles. Thecovalent linking of the polymer to the wells is helpful for maintainingthe gel in the structured features throughout the lifetime of thestructured substrate during a variety of uses. However in manyembodiments, the gel need not be covalently linked to the wells. Forexample, in some conditions silane free acrylamide (SFA, see, forexample, U.S. Pat. No. 8,563,477) which is not covalently attached toany part of the structured substrate, may be used as the gel material.

In particular embodiments, a structured substrate may be made bypatterning a solid support material with wells (e.g. microwells ornanowells), coating the patterned support with a gel material (e.g.PAZAM, SFA or chemically modified variants thereof, such as theazidolyzed version of SFA (azido-SFA)) and polishing the gel coatedsupport, for example via chemical or mechanical polishing, therebyretaining gel in the wells but removing or inactivating substantiallyall of the gel from the interstitial regions on the surface of thestructured substrate between the wells. Primer nucleic acids may beattached to gel material. A solution of target nucleic acids (e.g. afragmented human genome) may then be contacted with the polishedsubstrate such that individual target nucleic acids will seed individualwells via interactions with primers attached to the gel material;however, the target nucleic acids will not occupy the interstitialregions due to absence or inactivity of the gel material. Amplificationof the target nucleic acids will be confined to the wells since absenceor inactivity of gel in the interstitial regions prevents outwardmigration of the growing nucleic acid colony. The process isconveniently manufacturable, being scalable and utilizing conventionalmicro- or nanofabrication methods.

The term “flowcell” as used herein refers to a chamber comprising asolid surface across which one or more fluid reagents may be flowed.Examples of flowcells and related fluidic systems and detectionplatforms that may be readily used in the methods of the presentdisclosure are described, for example, in Bentley et al., Nature456:53-59 (2008), WO 04/018497; U.S. Pat. No. 7,057,026; WO 91/06678; WO07/123744; U.S. Pat. Nos. 7,329,492; 7,211,414; 7,315,019; 7,405,281,and US 2008/0108082.

In some embodiments, the solid support or its surface is non-planar,such as the inner or outer surface of a tube or vessel. In someembodiments, the solid support comprises microspheres or beads. By“microspheres” or “beads” or “particles” or grammatical equivalentsherein is meant small discrete particles. Suitable bead compositionsinclude, but are not limited to, plastics, ceramics, glass, polystyrene,methylstyrene, acrylic polymers, paramagnetic materials, thoria sol,carbon graphite, titanium dioxide, latex or cross-linked dextrans suchas Sepharose, cellulose, nylon, cross-linked micelles and Teflon®, aswell as any other materials outlined herein for solid supports may allbe used. “Microsphere Detection Guide” from Bangs Laboratories, FishersInd. is a helpful guide. In certain embodiments, the microspheres aremagnetic microspheres or beads.

The beads need not be spherical; irregular particles may be used.Alternatively or additionally, the beads may be porous. The bead sizesrange from nanometers, i.e. 100 nm, to millimeters, i.e. 1 mm, withbeads from about 0.2 micron to about 200 microns being preferred, andfrom about 0.5 to about 5 micron being particularly preferred, althoughin some embodiments smaller or larger beads may be used.

Clustered arrays may be prepared using either a process ofthermocycling, as described in WO/9844151, or a process whereby thetemperature is maintained as a constant, and the cycles of extension anddenaturing are performed using changes of reagents. Such isothermalamplification methods are described in patent application numbersWO/0246456 and US 2008/0009420. Due to the lower temperatures requiredin the isothermal process, this is particularly preferred.

It will be appreciated that any of the amplification methodologiesdescribed herein or generally known in the art may be utilized withuniversal or target-specific primers to amplify immobilized DNAfragments. Suitable methods for amplification include, but are notlimited to, the polymerase chain reaction (PCR), strand displacementamplification (SDA), transcription mediated amplification (TMA) andnucleic acid sequence based amplification (NASBA), as described in U.S.Pat. No. 8,003,354, which is incorporated herein by reference in itsentirety. The above amplification methods may be employed to amplify oneor more nucleic acids of interest. For example, PCR, including multiplexPCR, SDA, TMA, NASBA and the like may be utilized to amplify immobilizedDNA fragments. In some embodiments, primers directed specifically to thepolynucleotide of interest are included in the amplification reaction.

Other suitable methods for amplification of polynucleotides may includeoligonucleotide extension and ligation, rolling circle amplification(RCA) (Lizardi et al., Nat. Genet. 19:225-232 (1998)) andoligonucleotide ligation assay (OLA) (See generally U.S. Pat. Nos.7,582,420, 5,185,243, 5,679,524 and 5,573,907; EP 0 320 308 B1; EP 0 336731 B1; EP 0 439 182 B1; WO 90/01069; WO 89/12696; and WO 89/09835)technologies. It will be appreciated that these amplificationmethodologies may be designed to amplify immobilized DNA fragments. Forexample, in some embodiments, the amplification method may includeligation probe amplification or oligonucleotide ligation assay (OLA)reactions that contain primers directed specifically to the nucleic acidof interest. In some embodiments, the amplification method may include aprimer extension-ligation reaction that contains primers directedspecifically to the nucleic acid of interest. As a non-limiting exampleof primer extension and ligation primers that may be specificallydesigned to amplify a nucleic acid of interest, the amplification mayinclude primers used for the GoldenGate assay (Illumina, Inc., SanDiego, Calif.) as exemplified by U.S. Pat. Nos. 7,582,420 and 7,611,869.

Exemplary isothermal amplification methods that may be used in a methodof the present disclosure include, but are not limited to, MultipleDisplacement Amplification (MDA) as exemplified by, for example Dean etal., Proc. Natl. Acad. Sci. USA 99:5261-66 (2002) or isothermal stranddisplacement nucleic acid amplification exemplified by, for example U.S.Pat. No. 6,214,587. Other non-PCR-based methods that may be used in thepresent disclosure include, for example, strand displacementamplification (SDA) which is described in, for example Walker et al.,Molecular Methods for Virus Detection, Academic Press, Inc., 1995; U.S.Pat. Nos. 5,455,166, and 5,130,238, and Walker et al., Nucl. Acids Res.20:1691-96 (1992) or hyper-branched strand displacement amplificationwhich is described in, for example Lage et al., Genome Res. 13:294-307(2003). Isothermal amplification methods may be used with thestrand-displacing Phi 29 polymerase or Bst DNA polymerase largefragment, 5′->3′ exo- for random primer amplification of genomic DNA.The use of these polymerases takes advantage of their high processivityand strand displacing activity. High processivity allows the polymerasesto produce fragments that are 10-20 kb in length. As set forth above,smaller fragments may be produced under isothermal conditions usingpolymerases having low processivity and strand-displacing activity suchas Klenow polymerase. Additional description of amplification reactions,conditions and components are set forth in detail in the disclosure ofU.S. Pat. No. 7,670,810, which is incorporated herein by reference inits entirety.

Another polynucleotide amplification method that is useful in thepresent disclosure is Tagged PCR which uses a population of two-domainprimers having a constant 5′ region followed by a random 3′ region asdescribed, for example, in Grothues et al. Nucleic Acids Res.21(5):1321-2 (1993). The first rounds of amplification are carried outto allow a multitude of initiations on heat denatured DNA based onindividual hybridization from the randomly-synthesized 3′ region. Due tothe nature of the 3′ region, the sites of initiation are contemplated tobe random throughout the genome. Thereafter, the unbound primers may beremoved and further replication may take place using primerscomplementary to the constant 5′ region.

In some embodiments, isothermal amplification can be performed usingkinetic exclusion amplification (KEA), also referred to as exclusionamplification (ExAmp). A nucleic acid library of the present disclosurecan be made using a method that includes a step of reacting anamplification reagent to produce a plurality of amplification sites thateach includes a substantially clonal population of amplicons from anindividual target nucleic acid that has seeded the site. In someembodiments the amplification reaction proceeds until a sufficientnumber of amplicons are generated to fill the capacity of the respectiveamplification site. Filling an already seeded site to capacity in thisway inhibits target nucleic acids from landing and amplifying at thesite thereby producing a clonal population of amplicons at the site. Insome embodiments, apparent clonality can be achieved even if anamplification site is not filled to capacity prior to a second targetnucleic acid arriving at the site. Under some conditions, amplificationof a first target nucleic acid can proceed to a point that a sufficientnumber of copies are made to effectively outcompete or overwhelmproduction of copies from a second target nucleic acid that istransported to the site. For example in an embodiment that uses a bridgeamplification process on a circular feature that is smaller than 500 nmin diameter, it has been determined that after 14 cycles of exponentialamplification for a first target nucleic acid, contamination from asecond target nucleic acid at the same site will produce an insufficientnumber of contaminating amplicons to adversely impactsequencing-by-synthesis analysis on an Illumina sequencing platform.

As demonstrated by the above example, amplification sites in an arraycan be, but need not be, entirely clonal in particular embodiments.Rather, for some applications, an individual amplification site can bepredominantly populated with amplicons from a first target nucleic acidand can also have a low level of contaminating amplicons from a secondtarget nucleic acid. An array can have one or more amplification sitesthat have a low level of contaminating amplicons so long as the level ofcontamination does not have an unacceptable impact on a subsequent useof the array. For example, when the array is to be used in a detectionapplication, an acceptable level of contamination would be a level thatdoes not impact signal to noise or resolution of the detection techniquein an unacceptable way. Accordingly, apparent clonality will generallybe relevant to a particular use or application of an array made by themethods set forth herein. Exemplary levels of contamination that can beacceptable at an individual amplification site for particularapplications include, but are not limited to, at most 0.1%, 0.5%, 1%,5%, 10% or 25% contaminating amplicons. An array can include one or moreamplification sites having these exemplary levels of contaminatingamplicons. For example, up to 5%, 10%, 25%, 50%, 75%, or even 100% ofthe amplification sites in an array can have some contaminatingamplicons. It will be understood that in an array or other collection ofsites, at least 50%, 75%, 80%, 85%, 90%, 95% or 99% or more of the sitescan be clonal or apparently clonal.

In some embodiments, kinetic exclusion can occur when a process occursat a sufficiently rapid rate to effectively exclude another event orprocess from occurring. Take for example the making of a nucleic acidarray where sites of the array are randomly seeded with target nucleicacids from a solution and copies of the target nucleic acid aregenerated in an amplification process to fill each of the seeded sitesto capacity. In accordance with the kinetic exclusion methods of thepresent disclosure, the seeding and amplification processes can proceedsimultaneously under conditions where the amplification rate exceeds theseeding rate. As such, the relatively rapid rate at which copies aremade at a site that has been seeded by a first target nucleic acid willeffectively exclude a second nucleic acid from seeding the site foramplification. Kinetic exclusion amplification methods can be performedas described in detail in the disclosure of U.S. Pub. No. 2013/0338042,which is incorporated herein by reference in its entirety.

Kinetic exclusion can exploit a relatively slow rate for initiatingamplification (e.g. a slow rate of making a first copy of a targetnucleic acid) vs. a relatively rapid rate for making subsequent copiesof the target nucleic acid (or of the first copy of the target nucleicacid). In the example of the previous paragraph, kinetic exclusionoccurs due to the relatively slow rate of target nucleic acid seeding(e.g. relatively slow diffusion or transport) vs. the relatively rapidrate at which amplification occurs to fill the site with copies of thenucleic acid seed. In another exemplary embodiment, kinetic exclusioncan occur due to a delay in the formation of a first copy of a targetnucleic acid that has seeded a site (e.g. delayed or slow activation)vs. the relatively rapid rate at which subsequent copies are made tofill the site. In this example, an individual site may have been seededwith several different target nucleic acids (e.g. several target nucleicacids can be present at each site prior to amplification). However,first copy formation for any given target nucleic acid can be activatedrandomly such that the average rate of first copy formation isrelatively slow compared to the rate at which subsequent copies aregenerated. In this case, although an individual site may have beenseeded with several different target nucleic acids, kinetic exclusionwill allow only one of those target nucleic acids to be amplified. Morespecifically, once a first target nucleic acid has been activated foramplification, the site will rapidly fill to capacity with its copies,thereby preventing copies of a second target nucleic acid from beingmade at the site.

An amplification reagent can include further components that facilitateamplicon formation and, in some cases, increase the rate of ampliconformation. An example is a recombinase. Recombinase can facilitateamplicon formation by allowing repeated invasion/extension. Morespecifically, recombinase can facilitate invasion of a target nucleicacid by the polymerase and extension of a primer by the polymerase usingthe target nucleic acid as a template for amplicon formation. Thisprocess can be repeated as a chain reaction where amplicons producedfrom each round of invasion/extension serve as templates in a subsequentround. The process can occur more rapidly than standard PCR since adenaturation cycle (e.g. via heating or chemical denaturation) is notrequired. As such, recombinase-facilitated amplification can be carriedout isothermally. It is generally desirable to include ATP, or othernucleotides (or in some cases non-hydrolyzable analogs thereof) in arecombinase-facilitated amplification reagent to facilitateamplification. A mixture of recombinase and single stranded binding(SSB) protein is particularly useful as SSB can further facilitateamplification. Exemplary formulations for recombinase-facilitatedamplification include those sold commercially as TwistAmp kits byTwistDx (Cambridge, UK). Useful components of recombinase-facilitatedamplification reagent and reaction conditions are set forth in U.S. Pat.Nos. 5,223,414 and 7,399,590, the contents of which are incorporatedherein by reference.

Another example of a component that can be included in an amplificationreagent to facilitate amplicon formation and in some cases to increasethe rate of amplicon formation is a helicase. Helicase can facilitateamplicon formation by allowing a chain reaction of amplicon formation.The process can occur more rapidly than standard PCR since adenaturation cycle (e.g. via heating or chemical denaturation) is notrequired. As such, helicase-facilitated amplification can be carried outisothermally. A mixture of helicase and single stranded binding (SSB)protein is particularly useful as SSB can further facilitateamplification. Exemplary formulations for helicase-facilitatedamplification include those sold commercially as IsoAmp kits fromBiohelix (Beverly, Mass.). Further, examples of useful formulations thatinclude a helicase protein are described in U.S. Pat. Nos. 7,399,590 and7,829,284, each of which is incorporated herein by reference.

Yet another example of a component that can be included in anamplification reagent to facilitate amplicon formation and in some casesincrease the rate of amplicon formation is an origin binding protein.

Use in Sequencing/Methods of Sequencing

The immobilized polynucleotides from the pooled libraries may besequenced in any suitable manner. Preferably, sequencing is performed bysequencing by synthesis in which nucleotides are added successively to afree 3′ hydroxyl group of a sequencing primer using the immobilizedpolynucleotides as a template, resulting in synthesis of apolynucleotide chain in the 5′ to 3′ direction. The nature of thenucleotide added is preferably determined after each nucleotideaddition. Sequencing techniques using sequencing by ligation, whereinnot every contiguous base is sequenced, and techniques such as massivelyparallel signature sequencing (MPSS) where bases are removed from,rather than added to the strands on the surface are also within thescope of the disclosure, as are techniques using detection ofpyrophosphate release (pyrosequencing). Such pyrosequencing basedtechniques are particularly applicable to sequencing arrays of beadswhere the beads have been amplified in an emulsion such that a singletemplate from the library molecule is amplified on each bead.

The initiation point for the sequencing reaction may be provided byannealing of a sequencing primer to a product of the solid-phaseamplification reaction. In this connection, one or both of the adaptersadded during formation of the template library may include a nucleotidesequence which permits annealing of a sequencing primer to immobilizedpolynucleotides, such as the adapter-target-adapter polynucleotides.

The index tag sequence and target sequence may be determined in a singleread from a single sequencing primer, or in multiple reads from morethan one sequencing primers. In the case of two reads from twosequencing primers, the “index tag read” and the “target read” may beperformed in either order, with a suitable denaturing step to remove theannealed primer after the first sequencing read is completed. Suitabledenaturing steps may include formamide, hydroxide or heat as generallyknown in the art.

The products of solid-phase amplification reactions where both forwardand reverse amplification primers are covalently immobilized on thesolid surface may be so-called “bridged” structures formed by annealingof pairs of immobilized polynucleotide strands and immobilizedcomplementary strands, both strands being attached to the solid supportat the 5′ end. Arrays comprised of such bridged structures provideinefficient templates for nucleic acid sequencing, since hybridizationof a conventional sequencing primer to one of the immobilized strands isnot favored compared to annealing of this strand to its immobilizedcomplementary strand under standard conditions for hybridization.Examples of bridged or cluster amplification are described in, forexample, U.S. Pat. Nos. 7,985,565 and 7,115,400.

In order to provide more suitable templates for nucleic acid sequencing,it is preferred to remove substantially all or remove or displace atleast a portion of one of the immobilized strands in the “bridged”structure to generate a template which is at least partiallysingle-stranded. The portion of the template which is single-strandedwill thus be available for hybridization to a sequencing primer. Theprocess of removing all or a portion of one immobilized strand in a“bridged” double-stranded nucleic acid structure may be referred toherein as ‘linearization’, and is described in further detail in WO2007/010251, WO 2006/064199, WO 2005/065814, WO 2015/106941, WO1998/044151, and WO 2000/018957.

Bridged template structures may be linearized by cleavage of one or bothstrands with a restriction endonuclease or by cleavage of one strandwith a nicking endonuclease. Other methods of cleavage may be used as analternative to restriction enzymes or nicking enzymes, including interalia chemical cleavage (e.g. cleavage of a diol linkage with periodate),cleavage of abasic sites by cleavage with endonuclease (for example‘USER’, as supplied by NEB, Cat # M5505S), or by exposure to heat oralkali, cleavage of ribonucleotides incorporated into amplificationproducts otherwise comprised of deoxyribonucleotides, photochemicalcleavage or cleavage of a peptide linker.

It will be appreciated that a linearization step may not be essential ifthe solid-phase amplification reaction is performed with only one primercovalently immobilized and the other in free solution.

Following the cleavage step, regardless of the method used for cleavage,the product of the cleavage reaction may be subjected to denaturingconditions in order to remove the portion(s) of the cleaved strand(s)that are not attached to the solid support. Suitable denaturingconditions, for example sodium hydroxide solution, formamide solution orheat, will be apparent to the skilled reader with reference to standardmolecular biology protocols (Sambrook et al., 2001, Molecular Cloning, ALaboratory Manual, 3rd Ed, Cold Spring Harbor Laboratory Press, ColdSpring Harbor Laboratory Press, NY; Current Protocols, eds. Ausubel etal.). Denaturation results in the production of a sequencing templatewhich is partially or substantially single-stranded. A sequencingreaction may then be initiated by hybridization of a sequencing primerto the single-stranded portion of the template.

Thus, in some embodiments, a sequencing reaction comprises hybridizing asequencing primer to a single-stranded region of a linearizedamplification product, sequentially incorporating one or morenucleotides into a polynucleotide strand complementary to the region ofamplified template strand to be sequenced, identifying the base presentin one or more of the incorporated nucleotide(s) and thereby determiningthe sequence of a region of the template strand.

One preferred sequencing method which may be used relies on the use ofmodified nucleotides having removable 3′ blocks, for example asdescribed in WO 2004/018497 and U.S. Pat. No. 7,057,026. Once themodified nucleotide has been incorporated into the growingpolynucleotide chain complementary to the region of the template beingsequenced there is no free 3′-OH group available to direct furthersequence extension and therefore the polymerase cannot add furthernucleotides. Once the nature of the base incorporated into the growingchain has been determined, the 3′ block may be removed to allow additionof the next successive nucleotide. By ordering the products derivedusing these modified nucleotides, it is possible to deduce the DNAsequence of the DNA template. Such reactions may be done in a singleexperiment if each of the modified nucleotides has a different labelattached thereto, known to correspond to the particular base, tofacilitate discrimination between the bases added during eachincorporation step. Alternatively, a separate reaction may be carriedout containing each of the modified nucleotides separately.

The modified nucleotides may carry a label to facilitate theirdetection. A fluorescent label, for example, may be used for detectionof modified nucleotides. Each nucleotide type may thus carry a differentfluorescent label, for example, as described in WO 2007/135368. Thedetectable label need not, however, be a fluorescent label. Any labelmay be used which allows the detection of an incorporated nucleotide.

One method for detecting fluorescently labelled nucleotides comprisesusing laser light of a wavelength specific for the labelled nucleotides,or the use of other suitable sources of illumination. The fluorescencefrom the label on the nucleotide may be detected by a CCD camera orother suitable detection means. Suitable instrumentation for recordingimages of clustered arrays is described in WO 2007/123744.

Of course, any other suitable sequencing method may be employed.Preferably, the sequencing method relies on successive incorporation ofnucleotides into a polynucleotide chain. Suitable alternative techniquesinclude, for example, pyrosequencing, FISSEQ (fluorescent in situsequencing), MPSS and sequencing by ligation-based methods, for exampleas described is U.S. Pat. No. 6,306,597.

The nucleic acid sample may be further analyzed to obtain a second readfrom the opposite end of the fragment. Methodology for sequencing bothends of a cluster are described in WO 2007/010252 and WO 2008/041002. Inone example, the series of steps may be performed as follows; generateclusters, linearize, hybridize first sequencing primer and obtain firstsequencing read. The first sequencing primer may be removed, a secondprimer hybridized and the index tag sequenced. The poly nucleotidestrand may then be “inverted” on the surface by synthesizing acomplementary copy from the remaining immobilized primers used incluster amplification. This process of strand resynthesize regeneratesthe double stranded cluster. The original template strand may beremoved, to linearize the resynthesized strand that may then be annealedto a sequencing primer and sequenced in a third sequencing run.

In the cases where strand re-synthesis is employed, both strands may beimmobilized to the surface in a way that allows subsequent release of aportion of the immobilized strand. This may be achieved through a numberof mechanisms as described in WO 2007/010251. For example, one primermay contain a uracil nucleotide, which means that the strand may becleaved at the uracil base using the enzymes uracil glycosylase (UDG)which removes the nucleoside base, and endonuclease VIII that excisesthe abasic nucleotide. This enzyme combination is available as USER™enzyme from New England Biolabs (Cat # M5505). The second primer maycomprise an 8-oxoguanine nucleotide, which is then cleavable by theenzyme FPG (NEB Cat # M0240). This design of primers provides control ofwhich primer is cleaved at which point in the process, and also where inthe cluster the cleavage occurs. The primers may also be chemicallymodified, for example with a disulfide or diol modification that allowschemical cleavage at specific locations.

Referring now to FIG. 1, a schematic drawing illustrating an embodimentof a process for producing 5′ modified and 3′ blocked templatepolynucleotides for immobilizing on a solid surface for sequencing isshown. In FIG. 1A, a double stranded target polynucleotide fragment isshown. Initial portions of adapters may be attached to the ends of thetarget by ligation (see FIG. 1B) or tagmentation. The portions of theadapters (ab) comprise a double stranded portion attached to the doublestranded target and single stranded portions extending away from thetarget to the 5′ and 3′ ends. A 5′ modified primer (B′) is configured tohybridize to a single stranded portion of the adapter (b) in proximityto the 3′ end (FIG. 1C). A polymerase may be used to extend the primerB′ using the portions of the adapter and the target as a template toproduce a complement of the portions of the adapter (a′) and the target(FIG. 1D, strands from FIG. 1C removed for purposes of convenience andclarity). A 5′ modified primer (A) is configured to hybridize to asingle stranded portion of the complement of the adapter portion (a′) inproximity to the 3′ end (FIG. 1E). A polymerase may be used to extendthe primer A using the portions of the complement of the adapters andtarget as a template to produce portions of the adapter (b) and thetarget (FIG. 1F, strands from FIG. 1E removed for purposes ofconvenience and clarity).

If the adapter portion that is added by, for example, ligation ortagmentation includes the library specific index tag sequence at alocation between the sequence for hybridization of the primers (A, B′)and the target (when the portion of the adapter is attached to thetarget), amplification (FIGS. 1C-F) with primers (A, B′) may beperformed on pooled target fragments from different libraries, providedthat each fragment from each library includes a portion of an adapterhaving a library specific index tag sequence in a similar location andeach portion of the adapter from each library has a sequence (orcomplement) to which primers (A, B′) may hybridize. Otherwise, eachlibrary should be amplified separately.

The resulting 5′ protected template (amplified adapter-target-amplifiedadapter) may be subjected to 3′ blocking to produce a 5′ and 3′protected template polynucleotide (FIG. 1G) for immobilizing on a solidsurface for sequencing. 3′ blocking may affect any polynucleotidepresent in solution with the 5′ protected template, including any otheramplification fragments or residual polynucleotides (not shown).Accordingly, if adaptor portions (ab) are amplified with primers (A, B),the amplified adapters that are not attached to the template (not shown)should also be 3′ blocked.

Exonuclease treatment may optionally be applied to the resultingmixture. Remaining unblocked or unprotected polynucleotides may bedegraded prior to immobilizing the template polynucleotides on a solidsurface.

Referring now to FIG. 2 a schematic drawing is shown of an adapter(amplified adapter) 100 that may be used or result during amplificationof the libraries in preparation for sequencing. The depicted adapter 100comprises a double-stranded region 110 and a non-complementarysingle-stranded region 120. The 5′ ends are modified (indicated by the“*”) to prevent degradation by an exonuclease, and the 3′ ends areblocked (indicated by the “X”). One depicted strand of the adapter 100comprises a universal extension primer sequence 130, an index tagsequence 132, and a sequencing primer sequence 134. The other depictedstrand of the adapter 100 comprises a universal extension primersequence 140, an index tag sequence 142, and a sequencing primersequence 144.

The universal extension primer sequences 130, 140 may hybridize toextension primer oligonucleotides attached to a solid surface forpurposes of amplification or sequencing (if the adapter 100 wereattached to a target polynucleotide). Universal extension primersequence 140, or a portion thereof, may also hybridize to a sequencingprimer for sequencing index tag sequence 142. Alternatively, the strandmay comprise a further sequencing primer sequence (not shown).

Sequencing primer sequence 134 may hybridize to a sequencing primer toallow sequencing of index tag sequence 132. Index tag sequence 142 andindex tag sequence 132 may be the same or different.

Sequencing primer sequence 144 may hybridize to a sequencing primer toallow sequencing of a target polynucleotide sequence (if attached to theadapter 100).

Sequencing primer sequences 134, 144 may hybridize to, for example, PCRprimers if the adapters are attached to a target in a multi-step processas described above.

It will be understood that a suitable adapter for used in variousembodiments described herein may have more or less sequence features, orother sequence features, than those described regarding FIG. 2.

Referring now to FIG. 3, a schematic drawing of a templatepolynucleotide 200 of a library having an adapter 100—template210—adapter 100 sequence is shown. The template polynucleotide 210 isdouble stranded and attached to a double stranded portion of the first100 and second 101 adapters. The 3′ends of the template polynucleotide200 are blocked and the 5′ ends are modified, e.g., as described above.

Referring now to FIG. 4, a schematic illustration of a process forcluster amplification of a template polynucleotide 200 from a library toa solid surface 300 to prepare for sequencing is shown. In the firstpanel, the template polynucleotide 200 having a modified 5′ end and ablocked 3′ end is hybridized to a first extension primer 310 attached tothe solid surface 300. For example, universal extension primer sequence140 depicted in FIG. 2 of the adapter portion may hybridize to the firstextension primer 310.

The first extension primer 310 comprises a free 3′ end, and thusnucleotides may be added to the 3′end using the template polynucleotide200 as a template to produce a copy template strand 201 (see secondpanel) attached to the solid surface 300 in the presence of a suitablepolymerase. The template strand 200 may be removed and the copy strand201 may hybridize with a second extension primer 320 attached to thesolid surface 300 (see third panel). For example, universal extensionprimer sequence 130 depicted in FIG. 2 of the adapter portion mayhybridize to the second extension primer 320.

The second extension primer 320 comprises a free 3′ end, and thusnucleotides may be added to the 3′end using the copy templatepolynucleotide 201 as a template to produce an amplified template strand202 (see fourth panel) attached to the solid surface 300 in the presenceof a suitable polymerase. Additional rounds of amplification may beperformed to produce a cluster of copy template strands 201 andamplified template strands 202.

For purposes of illustration, the fifth panel of FIG. 4 depicts the copy201 and amplified 202 template strands in linear form.

Referring now to FIG. 5, a schematic drawing illustrating how blockingof 3′ ends (to prevent extension from the blocked 3′ end) may mitigateindex hopping is shown. The first two panels of FIG. 5 are the same asthe first two panels of FIG. 4. As shown in the third panel of FIG. 5, aresidual unincorporated (not attached to a target polynucleotide)adapter strand 104 may hybridize to an adapter portion of the copytemplate strand 201 (for example, the hybridization may occur at thedouble stranded region of the adapter and the adapter portion of thetemplate polynucleotide). The adapter strand 104 may be from a librarydifferent than the library from which the copy template strand 201 isderived. Accordingly, the adapter 104 may have an index tag sequencethat is different than the index tag sequence associated with the copytemplate strand 201. Because the 3′ end of the adapter is blocked(indicated by the “X”), the adapter 104 cannot serve as an effectiveprimer to extend and copy the copy template strand 201. However, ifextension were permitted (and the 3′ end of the unincorporated adapter104 were not blocked), a copy would be produced in which an incorrectindex tag (index tag from adapter 104 from a second library) would beassociated with a target polynucleotide from another library (targetpolynucleotide of template polynucleotide 201 from a first library). Ina subsequent round of amplification, an incorrectly indexedpolynucleotide could be attached to the surface 300.

Referring now to FIG. 6, a schematic drawing illustrating howexonuclease treatment to remove unblocked and unincorporated adapters oradapter strands may mitigate index hopping is shown. The first twopanels of FIG. 6 are the same as the first two panels of FIG. 4. Asshown in the bottom left panel of FIG. 6, an adapter strand 104 that mayresult from amplification (e.g., as described regarding FIGS. 1B-F) thatwas not blocked during a 3′ blocking step (e.g., as described regardingFIG. 1G) may hybridize to an adapter portion of the copy template strand201 (for example, the hybridization may occur at the double strandedregion of the adapter and the adapter portion of the templatepolynucleotide). The adapter strand 104 may be from a library differentthan the library from which the copy template strand 201 is derived.Accordingly, the adapter strand 104 may have an index tag sequence thatis different than the index tag sequence associated with the copytemplate strand 201. The adapter strand 104 may serve as an effectiveprimer to extend and copy the copy template strand 201. An amplifiedstrand would be produced in which an incorrect index tag (index tag fromadapter strand 104 from a second library) would be associated with atarget polynucleotide from another library (target polynucleotide oftemplate polynucleotide 201 from a first library). In a subsequent roundof amplification, an incorrectly indexed polynucleotide could beattached to the surface 300. However and as illustrated in the bottomright panel of FIG. 6, if the unblocked adapters or adapter strands thatmay result are digested by exonuclease treatment, the adapter strand isnot available to serve as an extension primer and index hoping ismitigated.

Referring now to FIGS. 7A and 7B, the nature of the index hoppingphenomenon is illustrated. FIG. 7A shows how reads from a given sampleare incorrectly demultiplexed and mixed with a different samplefollowing demultiplexing. FIG. 7B demonstrates index hopping in a dualindex system, where it leads to unexpected combinations of index tagsequences.

Referring now to FIGS. 8A and 8B, the general approach to measuring therate of index hopping in a given system is illustrated. FIG. 8A shows anexemplary layout of a dual adapter plate, wherein each individual wellof a 96-well plate contains a unique pair of index tag sequences (12different P7 indices combined with 8 different P5 indices). FIG. 8Bshows an experimental setup aimed at measuring the rate of indexhopping, wherein 8 unique dual index tag combinations are used (i.e. noP5 index is expected to pair up with more than one P7 index and viceversa). Unexpected combinations of index tags (e.g., D505-D703) are theneasily identified as instances of index hopping.

Referring now to FIGS. 9A and 9B, the effect of unligated adapters onthe rate of index hopping is illustrated. FIG. 9A shows a 6-foldincrease in index hopping associated with a 50% spike-in of freeadapters. FIG. 9B shows an approximately linear effect of the freeforked adapter on the rate of index hopping within the range tested. Theinventors also observed a more pronounced effect of free single-strandedP7 adapters on the rate of index hopping compared to freesingle-stranded P5 adapters (data not shown).

EXAMPLES Example 1: Sample Protocol for 3′ Blocking of 5′ ProtectedIndexed Libraries

This protocol explains how to perform a 3′ blocking treatment of 5′protected DNA libraries, to reduce index hopping. This method isdesigned to be performed on DNA library pools prior to the denaturationstep and subsequent cluster generation using the Illumina HiSeq® 4000and similar sequencing platforms utilizing patterned flow cells andExAmp based clustering (e.g., HiSeq® X and NovaSeq®).

Index hopping has been seen to occur where incorrect index sequences areassigned to the insert sequence resulting in sample misassignment.Performing this treatment on DNA sample pools before running on HiSeq®4000 should reduce the index hopping levels by some level which cannotat this stage be predicted consistently.

Treatment workflow may be considered to involve four steps: (i) produceDNA sample pool; (ii) perform treatment, (iii) cleanup sample andquantify; and (iv) cluster and sequence sample pool.

Consumables/Equipment:

Consumables and equipment may be supplied by a sequencing user ormanufacture. User supplied consumables may include a DNA library samplepool—30 μl at concentration to be used for denaturation duringclustering. The user may also supply freshly prepared 80% ethanol(EtOH).

Table 1 below illustrates some consumables and equipment that may beused.

TABLE 1 Consumables and Equipment Consumable/Equipment Supplier Ethanol200 proof (absolute) for Sigma-Aldrich, Cat #E7023 molecular biologyMagnetic stand-96 Life Technologies, Cat #AM10027 Vortexer General labsupplier 96-well thermal cycler (with General lab supplier heated lid)

A sequencing manufacturer may supply BMX (Blocking Mix), EMX(Exonuclease Mix), RSB (Resuspension Buffer), and SPB (SamplePurification Beads).

The EMX may include an exonuclease buffer (67 mM Glycine-KOH, 2.5 mMMgCl₂, 50 μg/ml BSA) and Lambda Exonuclease (New England Biolabs, Cat #M0262S/L).

The BMX may include a sequencing premix (Tris buffer, sodium chloride,sucrose, magnesium sulfate, EDTA and Tween 20), a ddNTP mix, Pol19 DNApolymerase, and TDT terminal transferase.

The RSB may include a Tris buffer, pH 8.5.

The SPB may include AgenCourt® AMPure® XP beads (Beckman Coulter, Cat #A63880). The SPB should be vortexed before each use. The SPB should bevortexed frequently to make sure that beads are evenly distributed. TheSPB should be aspirated and dispensed slowly due to the viscosity of thesolution.

Some of the consumables should be stored and prepared as indicated inTable 2 below.

TABLE 2 Storage and preparation of consumables Item Storage InstructionsBMX −25° C. to −15° C. Thaw at room temperature, and then place on ice.Return to storage after use. EMX −25° C. to −15° C. Thaw at roomtemperature, and then place on ice. Return to storage after use. RSB 2°C. to 8° C. Let stand for 30 min to bring to room temperature. SPB 2° C.to 8° C. Let stand for 30 min to bring to room temperature.

The following EMX program may be saved on the thermal cycler: (i) choosethe preheat lid option and set to 100° C.; (ii) 37° C. for 30 mins;(iii) 75° C. for 10 mins; and (iv) hold at 4° C.

The following BMX program may be saved on the thermal cycler: (i) choosethe preheat lid option and set to 100° C.; (ii) 38° C. for 20 mins;(iii) 60° C. for 20 mins; and (iv) hold at 4° C.

For the 3′ blocking treatment, the samples may be treated as follows:(i) centrifuge BMX at 600×g for 5 seconds; (ii) add 30 μl of 5′protected DNA library sample pool to PCR tube; (iii) add 30 μl BMX toeach sample in each PCR tube and then mix thoroughly by pipetting up anddown; (iv) incubate by placing on the thermal cycler and running the BMXprogram. Each tube contains 60 μl.

For the 3′ blocking plus exonuclease treatment, the samples may betreated as follows: (i) centrifuge EMX at 600×g for 5 seconds; (ii) add27 μl of 5′ protected DNA library sample pool to PCR tube; (iii) add 5μl EMX to each sample in each PCR tube and then mix thoroughly bypipetting up and down; (iv) incubate by placing on the thermal cyclerand running the EMX program; (v) centrifuge BMX at 600×g for 5 seconds;(vi) add 32 μl BMX directly to each exonuclease reaction in each PCRtube and then mix thoroughly by pipetting up and down; and (vii)incubate by placing on the thermal cycler and running the BMX program.Each tube contains 64 μl.

The treated pooled sample may be cleaned up as follows: (1) vortex SPBuntil well-dispersed; (2) add 60 μl SPB to each sample treatment tubeand mix thoroughly by pipetting up and down; (3) incubate at roomtemperature for 5 minutes; (4) place on a magnetic stand and wait untilthe liquid is clear (2-5 minutes); (5) remove and discard allsupernatant from each tube; (6) wash 2 times as follows: (a) add 200 μlfreshly prepared 80% EtOH to each tube, (b) incubate on the magneticstand for 30 seconds, and (c) remove and discard all supernatant fromeach tube; (7) use a 20 μl pipette to remove residual EtOH from eachtube; (8) air-dry on the magnetic stand for 5 minutes; (9) add 22.5 μlRSB to each tube; (10) remove from the magnetic stand and then mixthoroughly by pipetting up and down; (11) incubate at room temperaturefor 2 minutes; (12) place on a magnetic stand and wait until the liquidis clear (2-5 minutes); (13) transfer 20 μl supernatant to a new tube;(14) quantify libraries if required and proceed onto standard clusteringfor the HiSeq® 4000 platform starting with NaOH denaturation step; and(15) store at −25° C. to −15° C. if not clustering immediately.

Example 2: Reduction of Index Hopping by 3′ Blocking of 5′ ProtectedIndexed Libraries

The treatment protocol set forth above in Example 1 was applied incombination with the following materials, equipment and methods forclustering and sequencing on Illumina platform.

Experimental Conditions:

(1) Human 450 bp NA12878 (Coriell Institute) TrueSeq® Nano librarygenerated using 5′ protected P5 and P7 primers loaded at 300 pM; (2)HiSeq® X instrument and Illumina SBS chemistry according tomanufacturer's instructions; (3) 550 nm ILS v3 flow cell; (4) ExAmpamplification as previously described; and (5) 50% adapter spike-in:free forked adapter from the Illumina dual adapter plate (DAP) spikedinto template library prior to denaturation, neutralization, ExAmp mixaddition and clustering.

Results of this experiment are summarized in Table 3 below and FIG. 10.

TABLE 3 Reduction of index hopping by PCR protection with 3′ blockingLibrary % Index Hopping Standard Adapters 2.4 5′, 3′ Protected Adapters0.03 Protected Adapters + Exonuclease 0.023

As illustrated above, index hopping was decreased significantly relativeto standard adapters by employing 5′ protected and 3′ blocked adaptersas described herein. Optional exonuclease treatment may have furtherreduced index hopping.

Any patent, patent application (whether published or not), or otherliterature referred to herein in hereby incorporated herein in itsrespective entirety or in part to the extent that it does not conflictwith the disclosure presented herein.

In addition to the documents already cited in this application,reference is hereby made to three provisional patent applicationsidentically entitled “Compositions and methods for improving sampleidentification in indexed nucleic acid libraries” that were filed on thesame day as the provisional application to which the present applicationclaims priority (U.S. Provisional Application Nos. 62/488,824,62/488,825, and 62/488,830, which were filed on Apr. 23, 2017). Theentire contents of these applications are also incorporated herein byreference.

It will be apparent to those skilled in the art that variousmodifications and variations may be made to the present inventivetechnology without departing from the spirit and scope of thedisclosure. Since modifications, combinations, sub-combinations andvariations of the disclosed embodiments incorporating the spirit andsubstance of the inventive technology may occur to persons skilled inthe art, the inventive technology should be construed to includeeverything within the scope of the appended claims and theirequivalents.

What is claimed is:
 1. A method, comprising: providing a first librarycomprising a first plurality of polynucleotides having a firstadapter-target-first adapter sequence, wherein the polynucleotides ofthe first plurality of polynucleotides are double stranded in a regioncomprising the target and at least a portion of the first adapter onboth ends of the target; providing a first primer oligonucleotideconfigured to hybridize with a portion of the first adapter in proximityto a 3′ end of a strand of the first adapter, wherein the 5′ end of thefirst primer oligonucleotide is modified to prevent digestion by anenzyme having 5′ exonuclease activity; providing a second primeroligonucleotide configured to hybridize with a complement of a portionof the first adapter in proximity to a 3′ end of a strand of thecomplement of the first adapter, wherein the 5′ end of the second primeroligonucleotide is modified to prevent digestion by an enzyme having 5′exonuclease activity; incubating the first library with the first andsecond primer oligonucleotides in a solution under conditions suitableto amplify the polynucleotides having a first adapter-target-firstadapter sequence to produce an amplified first library ofpolynucleotides having 5′ ends modified to prevent digestion by anenzyme having 5′ exonuclease activity, wherein the amplifiedpolynucleotides have an amplified first adapter-target-amplified firstadapter sequence, and wherein the amplified first adapter sequencecomprises a first library-specific sequence; modifying 3′ ends of theamplified first library of polynucleotides to prevent one or both of (i)digestion by an enzyme having 3′ exonuclease activity, or (ii) additionof nucleotides to the 3′ end by an enzyme having polymerase activity,thereby generating a protected first library of polynucleotides havingmodified 5′ and 3′ ends.
 2. The method according to claim 1, whereinmodifying the 3′ ends of the amplified first library of polynucleotidescomprises incorporating a dideoxynucleotide at the 3′ ends of thepolynucleotides.
 3. The method according to claim 1, wherein the 5′ endsof the amplified first library of polynucleotides comprise aphosphorothioate bond.
 4. The method according to claim 1, wherein the5′ ends of the amplified first library of polynucleotides comprise threephosphorothioate bonds.
 5. The method according to claim 1, furthercomprising incubating the protected first library of polynucleotideshaving modified 3′ ends with one or more enzymes having 5′ exonucleaseactivity and 3′ exonuclease activity.
 6. The method according to claim1, further comprising providing a substrate having a surface comprisinga plurality of attached oligonucleotides having free 3′ ends; andcontacting the surface of the substrate with a composition comprisingthe protected first library of polynucleotides having modified 3′ endsunder conditions that permit hybridization of a portion of a strand ofthe first adapter of the protected first library of polynucleotides toat least a portion of the oligonucleotides attached to the surface ofthe substrate.
 7. The method according to claim 6, further comprisingextending the oligonucleotides attached to the surface of the substratefrom the free 3′ end by incorporating nucleotides complementary to asequence of the protected first library of polynucleotides having themodified 3′ ends that are hybridized to the attached oligonucleotides toproduce a copy of the hybridized polynucleotide such that the copy isattached to the surface of the substrate.
 8. The method according toclaim 7, further comprising amplifying the copy attached to the surfaceof the substrate.
 9. The method according to claim 1, furthercomprising: providing a second library comprising a plurality ofpolynucleotides having a second adapter-target-second adapter sequence,wherein the polynucleotides of the second plurality of polynucleotidesare double stranded in a region comprising the target and at least aportion of the second adapter on both ends of the target; providing athird primer oligonucleotide configured to hybridize with a portion ofthe second adapter in proximity to a 3′ end of a strand of the secondadapter, wherein the 5′ end of the third primer oligonucleotide ismodified to prevent digestion by an enzyme having 5′ exonucleaseactivity; providing a fourth primer oligonucleotide configured tohybridize with a complement of a portion of the second adapter inproximity to a 3′ end of a strand of the complement of the secondadapter, wherein the 5′ end of the fourth primer oligonucleotide ismodified to prevent digestion by an enzyme having 5′ exonucleaseactivity; incubating the second library with the third and fourth primeroligonucleotides in a solution under conditions suitable to amplify thepolynucleotides having a second adapter-target-second adapter sequenceto produce an amplified second library of polynucleotides having 5′ endsmodified to prevent digestion by an enzyme having 5′ exonucleaseactivity, wherein the amplified polynucleotides have an amplified secondadapter-target-amplified second adapter sequence, and wherein theamplified second adapter sequence comprises a second library-specificsequence; modifying 3′ ends of the amplified second library ofpolynucleotides to prevent one or both of (i) digestion by an enzymehaving 3′ exonuclease activity, or (ii) addition of nucleotides to the3′ end by an enzyme having polymerase activity, thereby generating aprotected second library of polynucleotides having modified 5′ and 3′ends.
 10. The method according to claim 9, wherein modifying the 3′ endsof the amplified second library of polynucleotides comprisesincorporating a dideoxynucleotide at the 3′ ends of the polynucleotides.11. The method according to claim 9, wherein the 5′ ends of theamplified second library of polynucleotides comprise a phosphorothioatebond.
 12. The method according to claim 9, wherein the 5′ ends of theamplified second library of polynucleotides comprise threephosphorothioate bonds.
 13. The method according to claim 9, furthercomprising incubating the protected second library of polynucleotideshaving modified 3′ ends with one or more enzymes having 5′ exonucleaseactivity and 3′ exonuclease activity.
 14. The method according to claim9, further comprising contacting the surface of the substrate with acomposition comprising the protected second library of polynucleotideshaving modified 3′ ends under conditions that permit hybridization of aportion of a strand of the second adapter of the protected secondlibrary of polynucleotides to at least a portion of the oligonucleotidesattached to the surface of the substrate.
 15. The method according toclaim 14, further comprising extending the oligonucleotides attached tothe surface of the substrate from the free 3′ end by incorporatingnucleotides complementary to a sequence of the protected second libraryof polynucleotides having the modified 3′ ends that are hybridized tothe attached oligonucleotides to produce a copy of the hybridizedpolynucleotide such that the copy is attached to the surface of thesubstrate.
 16. The method according to claim 15, further comprisingamplifying the copy attached to the surface of the substrate.
 17. Themethod according to claim 1, wherein the first adapter sequencecomprises the first library-specific sequence.
 18. The method accordingto claim 17, further comprising: providing a second library comprising aplurality of polynucleotides having a second adapter-target-secondadapter sequence, wherein the polynucleotides of the second pluralityare double stranded in a region comprising the target and at least aportion of the second adapter on either end of the target, wherein thesecond adapter comprises a second library-specific sequence, wherein thefirst primer oligonucleotide is configured to hybridize with a portionof the second adapter in proximity to a 3′ end of a strand of the secondadapter, and wherein the second primer oligonucleotide is configured tohybridize with a complement of a portion of the second adapter inproximity to a 3′ end of a strand of the complement of the secondadapter; and incubating the second library in the solution with thefirst library with the first and second primer oligonucleotides toamplify the polynucleotides having the second adapter-target-secondadapter sequence to produce an amplified second library ofpolynucleotides having 5′ ends modified to prevent digestion by anenzyme having 5′ exonuclease activity, wherein modifying 3′ ends of theamplified first library of polynucleotides further comprises modifyingthe amplified second library of polynucleotides to prevent one or bothof (i) digestion by an enzyme having 3′ exonuclease activity, or (ii)addition of nucleotides to the 3′ end by an enzyme having polymeraseactivity, thereby generating a protected second library ofpolynucleotides having modified 5′ and 3′ ends.
 19. The method accordingto claim 1, further comprising incubating a composition comprising theprotected first library of polynucleotides having modified 5′ and 3′ends with an exonuclease.